Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003170.1 Hibiscus syriacus cultivar Beakdansim tig00006666_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: 749787
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 1 of 3
Found at i:655 original size:9 final size:9
Alignment explanation
Indices: 621--660 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
611 TTTTATTATT
621 TATTTAATAA
1 TATTTAAT-A
*
631 TATTTATATG
1 TATTTA-ATA
641 TATTTAATA
1 TATTTAATA
650 TATTTAATA
1 TATTTAATA
659 TA
1 TA
661 ATAGTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 13 0.48
10 12 0.44
11 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
TATTTAATA
Found at i:679 original size:3 final size:3
Alignment explanation
Indices: 654--753 Score: 91
Period size: 3 Copynumber: 33.7 Consensus size: 3
644 TTAATATATT
* * *
654 TAA T-A TAA TAG TAA TATA TAA TAA TAC TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
699 TAA T-A TAA TGA T-A TAG TAAA TAA TAA TAA T-A TAA TTAA TAA TAT
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA
743 TAA TAA TAA TA
1 TAA TAA TAA TA
754 TGGATAAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
2 8 0.10
3 63 0.80
4 8 0.10
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1296 original size:111 final size:113
Alignment explanation
Indices: 1088--1565 Score: 853
Period size: 113 Copynumber: 4.3 Consensus size: 113
1078 TATGAACTCT
* * * *
1088 CTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTC-CGAAAAGATAATCCATCAATTGATGGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
1151 TTCAGGT-AAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTC
66 TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1197 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGATGATCCATC-AGTGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
1261 TTCAGGT-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
66 TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1308 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
1373 TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
66 TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1421 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGATGATCCATCAAGTGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
1485 TTCAGGTAAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
66 TTCAGGTAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
1534 CTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACT
1566 CGAACTGGAA
Statistics
Matches: 357, Mismatches: 6, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
109 31 0.09
110 29 0.08
111 97 0.27
112 53 0.15
113 147 0.41
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
Found at i:1446 original size:224 final size:223
Alignment explanation
Indices: 1088--1565 Score: 847
Period size: 224 Copynumber: 2.1 Consensus size: 223
1078 TATGAACTCT
* *
1088 CTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCCGAAAAGATAATCCATCAATTGATGGAT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCCGAAAAGATAATCCATCAAGTGATGAAT
1152 TCAGGTAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
66 TCAGGTAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1217 TCATTATGAACTTTTTCTGGAAAAGATGATCCATC-AGTGATGAATTCAGGT-AAAGG-TTGAAC
131 TCATTATGAACTTTCTCTGG-AAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTTGAAC
1279 AAATTCTTCTCATTATGAACTTCTTCTTC
195 AAATTCTTCTCATTATGAACTTCTTCTTC
* *
1308 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC-CGAAAAGATAATCCATCAAGTGATGAA
1373 TTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
65 TTCAGGT-AAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC
1438 TTCTCATTATGAACTTTCTCTGGAAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTTGA
128 TTCTCATTATGAACTTTCTCTGGAAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTTGA
1503 ACAAATTCTTCTCATTATGAACTTCTTCTTC
193 ACAAATTCTTCTCATTATGAACTTCTTCTTC
1534 CTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACT
1566 CGAACTGGAA
Statistics
Matches: 246, Mismatches: 5, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
220 31 0.13
221 5 0.02
222 30 0.12
223 25 0.10
224 83 0.34
225 5 0.02
226 67 0.27
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (223 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCCGAAAAGATAATCCATCAAGTGATGAAT
TCAGGTAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGAAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTTGAACA
AATTCTTCTCATTATGAACTTCTTCTTC
Found at i:2679 original size:83 final size:83
Alignment explanation
Indices: 2299--2844 Score: 926
Period size: 83 Copynumber: 6.6 Consensus size: 83
2289 TCCTACTGAA
* *
2299 CAGATCAGATAACT--AAGAACACTTCCAGAAGATACTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
2361 ATGATTGGTTTTGTC-AAC
65 ATGATTGGTTTTGTCAAAC
*
2379 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
2443 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
2462 CAGATCAGATAACTC-AAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAA-TCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
2525 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
*
2543 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
*
2608 ATGATTGGATTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
2627 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
*
2692 TGATTGGTTCTGTCAAAC
66 TGATTGGTTTTGTCAAAC
2710 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
*
2775 TGATTGGTTTTGTCAAAT
66 TGATTGGTTTTGTCAAAC
* * *
2793 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGTAAATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCAT
2845 TTGTTCTATT
Statistics
Matches: 447, Mismatches: 12, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
80 14 0.03
81 37 0.08
82 127 0.28
83 207 0.46
84 62 0.14
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:3519 original size:18 final size:16
Alignment explanation
Indices: 3498--3538 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
3488 AGAAAAGAAT
3498 AATTGAATTTCCAAAATA
1 AATTGAATTT-C-AAATA
*
3516 AATTTAATTTCAAATA
1 AATTGAATTTCAAATA
3532 AATTGAA
1 AATTGAA
3539 CTTGAAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 11 0.52
17 1 0.05
18 9 0.43
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (16 bp):
AATTGAATTTCAAATA
Found at i:16514 original size:20 final size:19
Alignment explanation
Indices: 16489--16533 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
16479 TATTTTTTAT
* *
16489 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
16509 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
16528 TATTTA
1 TATTTA
16534 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:16523 original size:26 final size:30
Alignment explanation
Indices: 16484--16539 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
16474 GCAATTATTT
*
16484 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
16511 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
16540 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:16540 original size:3 final size:3
Alignment explanation
Indices: 16532--16647 Score: 178
Period size: 3 Copynumber: 38.7 Consensus size: 3
16522 TTAATATATT
*
16532 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
16580 TGA TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
16628 TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
16648 TGGATAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:24092 original size:32 final size:32
Alignment explanation
Indices: 24050--24111 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
24040 ATACTTAATT
* *
24050 TTTTTATATTTAAAATATTTGCAACCTAAAAA
1 TTTTAATATTTAAAATATTTACAACCTAAAAA
24082 TTTTAATATTTAAAATATTTACAACCTAAA
1 TTTTAATATTTAAAATATTTACAACCTAAA
24112 CACATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTTAATATTTAAAATATTTACAACCTAAAAA
Found at i:27980 original size:31 final size:29
Alignment explanation
Indices: 27945--28014 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
27935 GAAAAATTAT
**
27945 TATTTTGGTCATTAAACTTTTCCTAAATTTA
1 TATTTTGGTCACCAAAC-TTTCC-AAATTTA
**
27976 TATTTTGACCACCAAACTTTCCAAATTTA
1 TATTTTGGTCACCAAACTTTCCAAATTTA
28005 TATTTTGGTC
1 TATTTTGGTC
28015 GGTTGTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 15 0.45
30 5 0.15
31 13 0.39
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (29 bp):
TATTTTGGTCACCAAACTTTCCAAATTTA
Found at i:34141 original size:18 final size:18
Alignment explanation
Indices: 34118--34170 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
34108 AGGGATTATC
34118 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
34136 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
* *
34154 AGTGATCATTCGGGACA
1 AGTGGTCCTTCGGGACA
34171 AATATTCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:59920 original size:27 final size:30
Alignment explanation
Indices: 59858--59918 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
59848 AAAATAAGTG
* *
59858 TAAATTATATTATTATTTTAAATAGGTATT
1 TAAATTATATTATTATTTTAAATAGATACT
*
59888 TAAATTATATTA-T-TTTTAAATATATACT
1 TAAATTATATTATTATTTTAAATAGATACT
59916 TAA
1 TAA
59919 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.54
29 1 0.04
30 12 0.43
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
TAAATTATATTATTATTTTAAATAGATACT
Found at i:60578 original size:30 final size:30
Alignment explanation
Indices: 60542--60598 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
60532 GAGAAATTTA
60542 ATGGCAGTTATGCTCCGAGCACCTGAGGTG
1 ATGGCAGTTATGCTCCGAGCACCTGAGGTG
60572 ATGGCAGTTATGCTCCGAGCACCTGAG
1 ATGGCAGTTATGCTCCGAGCACCTGAG
60599 ATGACAACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.32, T:0.23
Consensus pattern (30 bp):
ATGGCAGTTATGCTCCGAGCACCTGAGGTG
Found at i:61641 original size:16 final size:17
Alignment explanation
Indices: 61604--61641 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
61594 TGATAAAAAA
*
61604 TTAAACAAATTAGTTGT
1 TTAAACAAATTAGTTAT
61621 TTAAACAAATTA-TTAT
1 TTAAACAAATTAGTTAT
61637 TTAAA
1 TTAAA
61642 TTAATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (17 bp):
TTAAACAAATTAGTTAT
Found at i:61813 original size:29 final size:29
Alignment explanation
Indices: 61780--61856 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 29
61770 AAAAAATCAG
61780 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
*
61809 TTAATTCGATTC-AGTTAATAATTTTCAAA
1 TTAATTCGGTTCGA-TTAATAATTTTCAAA
* *
61838 TAAATTTTGGTTCGATTAA
1 TTAA-TTCGGTTCGATTAA
61857 CATAACTGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.02
29 29 0.71
30 10 0.24
31 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:83607 original size:43 final size:44
Alignment explanation
Indices: 83559--83652 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
83549 AAATTACATT
* * * * *
83559 TTTATTTATT-TTTTAAATTTAGTCATTTCACCTCGGTTCACTC
1 TTTATTTATTGTTTTAAATATAATCATTTCACATCAGTCCACTC
*
83602 TTTATTT-TTGTTTTAAATATAATCGTTTCACATCAGTCCACTC
1 TTTATTTATTGTTTTAAATATAATCATTTCACATCAGTCCACTC
83645 TTTATTTA
1 TTTATTTA
83653 ATTAATATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.53
Consensus pattern (44 bp):
TTTATTTATTGTTTTAAATATAATCATTTCACATCAGTCCACTC
Found at i:84233 original size:23 final size:22
Alignment explanation
Indices: 84197--84262 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
84187 TTATAATATG
*
84197 TATATATATATTAACTTAAAAA
1 TATATTTATATTAACTTAAAAA
* *
84219 TATCTTTTATATTAACTTATTAAA
1 TAT-ATTTATATTAACTTA-AAAA
84243 TATATTTATTATTAACTTAA
1 TATATTTA-TATTAACTTAA
84263 TTTAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 3 0.08
23 17 0.47
24 16 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATTTATATTAACTTAAAAA
Found at i:84267 original size:26 final size:24
Alignment explanation
Indices: 84212--84280 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 24
84202 ATATATTAAC
*
84212 TTAAAAATATCTTTTATATTAACTTA
1 TTAAAAATAT-TTAT-TATTAACTTA
*
84238 TTAAATATATTTATTATTAACTTAA
1 TTAAAAATATTTATTATTAACTT-A
84263 TTTAAAAATATTT-TTATT
1 -TTAAAAATATTTATTATT
84281 TTCATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 9 0.24
25 9 0.24
26 20 0.53
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAAAATATTTATTATTAACTTA
Found at i:84302 original size:20 final size:20
Alignment explanation
Indices: 84262--84311 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
84252 TATTAACTTA
*
84262 ATTTAAAAATATTTTTATTTT
1 ATTTAAAAATA-TTATATTTT
84283 CATTTAAAAATA-TATATTTT
1 -ATTTAAAAATATTATATTTT
84303 ATGTTAAAA
1 AT-TTAAAA
84312 TTTATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 13 0.50
22 11 0.42
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTAAAAATATTATATTTT
Found at i:87983 original size:223 final size:224
Alignment explanation
Indices: 87596--88039 Score: 856
Period size: 223 Copynumber: 2.0 Consensus size: 224
87586 GTGATATTAG
87596 AGAACAGGCTGACCTCGAGGAAGTGGTCAGCTATTCGATAGAGCCTGTGCTACTGATATCATTGA
1 AGAACAGGCTGACCTCGAGGAAGTGGTCAGCTATTCGATAGAGCCTGTGCTACTGATATCATTGA
87661 TGTTGAAGCTGTTGAAGATGATGTAATTGAATCTTCTGCTACAGAATTTGCAGAGGTTTGCTTCT
66 TGTTGAAGCTGTTGAAGATGATGTAATTGAATCTTCTGCTACAGAATTTGCAGAGGTTTGCTTCT
87726 CTTGTTCAATATTTTTTTTTCTTCTCTTTAACTGTATGTGACATCTG-TTTTATGGATTCGTTTC
131 CTTGTTCAATATTTTTTTTTCTTCTCTTTAACTGTATGTGACATCTGTTTTTATGGATTCGTTTC
87790 AATCATGGGTGTTAATAATT-CTAGGCTT
196 AATCATGGGTGTTAATAATTCCTAGGCTT
87818 AGAACAGGCTGACCTCGAGGAAGTGGTCAGCTATTCGATAGAGCCTGTGCTACCTGATATCATTG
1 AGAACAGGCTGACCTCGAGGAAGTGGTCAGCTATTCGATAGAGCCTGTGCTA-CTGATATCATTG
87883 ATGTTGAAGCTGTTGAAGATGATGTAATTGAATCTTCTGCTACAGAATTTGCAGAGGTTTGCTTC
65 ATGTTGAAGCTGTTGAAGATGATGTAATTGAATCTTCTGCTACAGAATTTGCAGAGGTTTGCTTC
87948 TCTTGTTCAATATTTTTTTTTCTTCTCTTTAACTGTATGTGACATCTGTTTTTATGGATTCGTTT
130 TCTTGTTCAATATTTTTTTTTCTTCTCTTTAACTGTATGTGACATCTGTTTTTATGGATTCGTTT
*
88013 CAATCATGGGTGTTACTAATTCCTAGG
195 CAATCATGGGTGTTAATAATTCCTAGG
88040 ATTTTATGTC
Statistics
Matches: 218, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
222 52 0.24
223 125 0.57
224 36 0.17
225 5 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (224 bp):
AGAACAGGCTGACCTCGAGGAAGTGGTCAGCTATTCGATAGAGCCTGTGCTACTGATATCATTGA
TGTTGAAGCTGTTGAAGATGATGTAATTGAATCTTCTGCTACAGAATTTGCAGAGGTTTGCTTCT
CTTGTTCAATATTTTTTTTTCTTCTCTTTAACTGTATGTGACATCTGTTTTTATGGATTCGTTTC
AATCATGGGTGTTAATAATTCCTAGGCTT
Found at i:94285 original size:65 final size:65
Alignment explanation
Indices: 94203--94330 Score: 193
Period size: 65 Copynumber: 2.0 Consensus size: 65
94193 GGGGGGGACG
* * * * * *
94203 AGATGGTCGTGAAATGAGTAAAGGGCCGTATGGGATGTGGAGGGGTGTCTTTTTGAGCCGGAACC
1 AGATGATCGTGAAATGAGTAAAGGGCCGAATGGGATATGGAGGGATGTCTTTCTGAGCAGGAACC
*
94268 AGATGATCGTGAAATGAGTAAATGGCCGAATGGGATATGGAGGGATGTCTTTCTGAGCAGGAA
1 AGATGATCGTGAAATGAGTAAAGGGCCGAATGGGATATGGAGGGATGTCTTTCTGAGCAGGAA
94331 TCTGGCTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (65 bp):
AGATGATCGTGAAATGAGTAAAGGGCCGAATGGGATATGGAGGGATGTCTTTCTGAGCAGGAACC
Found at i:95053 original size:50 final size:50
Alignment explanation
Indices: 94978--95103 Score: 189
Period size: 50 Copynumber: 2.5 Consensus size: 50
94968 TTAGCAATAA
* **
94978 AGCGCGCCCCCTGCACCGCTCTATACGATGATTTGACGCCACGTAGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGGTGACGCCACGTAGGTAT
* *
95028 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGGTGACGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGGTGACGCCACGTAGGTAT
* *
95078 AGCGCGGCCCCTGCAGCGCGCTATAC
1 AGCGCGCCCCCTGCACCGCGCTATAC
95104 ATGTATATCT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.17, C:0.36, G:0.29, T:0.17
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGGTGACGCCACGTAGGTAT
Found at i:95518 original size:110 final size:111
Alignment explanation
Indices: 95378--95598 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 111
95368 TGGAAATCAT
* *
95378 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
95443 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
95488 ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
95553 TAATTAGTTGATTCATTTAATGTATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
95599 TTTTTGTAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 70 0.69
111 32 0.31
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:97127 original size:18 final size:18
Alignment explanation
Indices: 97104--97143 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
97094 CCAGCAGCCA
97104 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
97122 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
97140 CCGC
1 CCGC
97144 CATCGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:97434 original size:3 final size:3
Alignment explanation
Indices: 97419--97449 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
97409 CCTGCGTAAA
*
97419 ACG ACG ACA ACG ACG ACG ACG ACG ACG ACG A
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG A
97450 TGGTGATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.32, G:0.29, T:0.00
Consensus pattern (3 bp):
ACG
Found at i:101179 original size:50 final size:51
Alignment explanation
Indices: 101103--101230 Score: 134
Period size: 51 Copynumber: 2.5 Consensus size: 51
101093 CCCTACGTGG
* * * ** **
101103 CGTATAGCGCGCTGTAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGCAGCGCTATACCCCACGTAACGCCAAATCAC
* * *
101153 CGTATAGCGCGGTGCAGGGGGAGCGCTATACCCCACTTAACGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGCAGCGCTATACCCCACGTAACGCCAAATCAC
*
101204 CGTATAACGCGGTGCAGGGCGC-GCGCT
1 CGTATAGCGCGGTGCAGGG-GCAGCGCT
101231 TTACTATTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
50 26 0.41
51 37 0.58
52 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGCAGCGCTATACCCCACGTAACGCCAAATCAC
Found at i:101732 original size:32 final size:32
Alignment explanation
Indices: 101674--101737 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
101664 TATTGTCAAG
*
101674 CTCGACTCGAACTCGAAAACTTTAAATATAAA
1 CTCGACTCGAACTCGAAAACTGTAAATATAAA
*
101706 CTCGACTCG-ACTCGAAAACTCGTAAATCTAAA
1 CTCGACTCGAACTCGAAAACT-GTAAATATAAA
101738 ATCTTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (32 bp):
CTCGACTCGAACTCGAAAACTGTAAATATAAA
Found at i:101885 original size:11 final size:11
Alignment explanation
Indices: 101825--101887 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
101815 AAATCAAAAA
*
101825 CTCGATTGAAG
1 CTCGATTCAAG
*
101836 CTCAGAACTCAAG
1 CTC-G-ATTCAAG
* *
101849 CTCAATTCAAA
1 CTCGATTCAAG
*
101860 CTCGATTTGAAG
1 CTCGA-TTCAAG
101872 CTCGATTCAAG
1 CTCGATTCAAG
101883 CTCGA
1 CTCGA
101888 CGGGTTAATG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
11 22 0.55
12 10 0.25
13 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:103974 original size:7 final size:7
Alignment explanation
Indices: 103931--103959 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
103921 AATCGAATTA
103931 AGGGATT
1 AGGGATT
103938 AGGGATT
1 AGGGATT
103945 AGGGATT
1 AGGGATT
103952 AGGGATT
1 AGGGATT
103959 A
1 A
103960 AGATTTAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (7 bp):
AGGGATT
Found at i:104728 original size:17 final size:17
Alignment explanation
Indices: 104706--104750 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
104696 TCGTTAAGAA
104706 CTCGAGTCGAGCTTGAG
1 CTCGAGTCGAGCTTGAG
104723 CTCGAGTCGAGCTTGAG
1 CTCGAGTCGAGCTTGAG
104740 CTCGAGTCGAG
1 CTCGAGTCGAG
104751 TCCATTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.22
Consensus pattern (17 bp):
CTCGAGTCGAGCTTGAG
Found at i:104752 original size:5 final size:6
Alignment explanation
Indices: 104706--104750 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
104696 TCGTTAAGAA
* *
104706 CTCGAG -TCGAG CTTGAG CTCGAG -TCGAG CTTGAG CTCGAG -TCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
104751 TCCATTCGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
5 15 0.45
6 18 0.55
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.22
Consensus pattern (6 bp):
CTCGAG
Found at i:105177 original size:24 final size:23
Alignment explanation
Indices: 105137--105190 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
105127 ATTATGTATA
*
105137 ATTTT-AAAAAATAAAAATTTAT
1 ATTTTAAAAAAATAAAAATTAAT
105159 ATTTTAAAACAAATAAAAATTAAT
1 ATTTTAAAA-AAATAAAAATTAAT
*
105183 AATTTAAA
1 ATTTTAAA
105191 TAATAGATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.18
23 3 0.11
24 20 0.71
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTTTAAAAAAATAAAAATTAAT
Found at i:106805 original size:16 final size:16
Alignment explanation
Indices: 106784--106833 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
106774 ATTATATTTG
106784 ATATTAAATAATTAGT
1 ATATTAAATAATTAGT
* *
106800 ATATTACATAGTT--T
1 ATATTAAATAATTAGT
* *
106814 ATATTATATATTTAGT
1 ATATTAAATAATTAGT
106830 ATAT
1 ATAT
106834 ACTATATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 12 0.43
16 16 0.57
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (16 bp):
ATATTAAATAATTAGT
Found at i:107802 original size:51 final size:50
Alignment explanation
Indices: 107729--107859 Score: 124
Period size: 51 Copynumber: 2.6 Consensus size: 50
107719 AATGTATTCA
* * *
107729 ACTATATAATATTCATACATATAGTATATACT-TTGA-ATTTATATAATTTAT
1 ACTATATAA-ATTAATATATATA-TATATACTATGGACA-TTATATAATTTAT
* * *
107780 ACTATATAAATTAATAGTATATAT-TATATGTATGGACATTCTATAGTTTAT
1 ACTATATAAATTAATA-TATATATATATA-CTATGGACATTATATAATTTAT
*
107831 ACTATATAATTTATATATATATATATATA
1 ACTATATAAATTA-ATATATATATATATA
107860 GTTTATATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
49 4 0.06
50 8 0.12
51 47 0.70
52 8 0.12
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (50 bp):
ACTATATAAATTAATATATATATATATACTATGGACATTATATAATTTAT
Found at i:107843 original size:14 final size:13
Alignment explanation
Indices: 107821--107968 Score: 51
Period size: 13 Copynumber: 11.4 Consensus size: 13
107811 ATGGACATTC
*
107821 TATAGTTTATACTA
1 TATAATTTATA-TA
107835 TATAATTTATATA
1 TATAATTTATATA
*
107848 TAT-ATATATATA
1 TATAATTTATATA
* * *
107860 GT-TTATATATACTG
1 -TATAATTTATA-TA
*
107874 TATAGTTTATATA
1 TATAATTTATATA
*
107887 TACTAA--TAAACTA
1 TA-TAATTTATA-TA
*
107900 TATAGTTTATATA
1 TATAATTTATATA
*
107913 TACTAA--TAAACTA
1 TA-TAATTTATA-TA
*
107926 TATAGTTTAT-TAA
1 TATAATTTATAT-A
**
107939 TATAAACTATATA
1 TATAATTTATATA
*
107952 TAT-ATATATATA
1 TATAATTTATATA
107964 TATAA
1 TATAA
107969 ACTATATAGT
Statistics
Matches: 99, Mismatches: 20, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
12 30 0.30
13 42 0.42
14 27 0.27
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (13 bp):
TATAATTTATATA
Found at i:107879 original size:18 final size:18
Alignment explanation
Indices: 107846--108005 Score: 83
Period size: 17 Copynumber: 9.3 Consensus size: 18
107836 ATAATTTATA
107846 TATATATA-TATATAGTT
1 TATATATACTATATAGTT
*
107863 TATATATACTGTATAGTT
1 TATATATACTATATAGTT
***
107881 TATATATACTA-ATAAAC
1 TATATATACTATATAGTT
* *
107898 TATATAGT-TTATATA-TAC
1 TATATA-TACTATATAGT-T
*
107916 TA-ATAAACTATATAGTT
1 TATATATACTATATAGTT
**
107933 TAT-TA-A-TATA-A-AC
1 TATATATACTATATAGTT
*
107946 TATATATA-TATATA-TA
1 TATATATACTATATAGTT
*
107962 TATATAAACTATATAGTT
1 TATATATACTATATAGTT
* *
107980 CATATATGCACTACATAGTT
1 TATATAT--ACTATATAGTT
108000 TATATA
1 TATATA
108006 CAATATATAA
Statistics
Matches: 109, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
13 3 0.03
14 3 0.03
15 9 0.08
16 9 0.08
17 38 0.35
18 32 0.29
20 15 0.14
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (18 bp):
TATATATACTATATAGTT
Found at i:107907 original size:26 final size:25
Alignment explanation
Indices: 107821--107986 Score: 155
Period size: 26 Copynumber: 6.6 Consensus size: 25
107811 ATGGACATTC
*
107821 TATAGTTTATACTATATAATTTATA-TA
1 TATAGTTTATA-TATATAA--TAAACTA
* * * *
107848 TATA-TATATATAGTTTATATATACTG
1 TATAGTTTATATA-TATA-ATAAACTA
107874 TATAGTTTATATATACTAATAAACTA
1 TATAGTTTATATATA-TAATAAACTA
107900 TATAGTTTATATATACTAATAAACTA
1 TATAGTTTATATATA-TAATAAACTA
107926 TATAGTTTAT-TA-AT-ATAAACTA
1 TATAGTTTATATATATAATAAACTA
*
107948 TATA-TATATATATATATATAAACTA
1 TATAGTTTATATATATA-ATAAACTA
*
107973 TATAGTTCATATAT
1 TATAGTTTATATAT
107987 GCACTACATA
Statistics
Matches: 119, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.03
22 14 0.12
23 3 0.03
24 1 0.01
25 20 0.17
26 63 0.53
27 14 0.12
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (25 bp):
TATAGTTTATATATATAATAAACTA
Found at i:107986 original size:2 final size:2
Alignment explanation
Indices: 107828--107967 Score: 65
Period size: 2 Copynumber: 67.0 Consensus size: 2
107818 TTCTATAGTT
* *
107828 TA TA CTA TA TA -A TT TA TA TA TA TA TA TA TA TA GTT 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
* * * *
107871 CTG TA TA GTT TA TA TA TA CTA -A TA AA CTA TA TA GTT 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
* * *
107915 CTA -A TA AA CTA TA TA GTT TA T- TA -A TA TA AA CTA 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
107956 TA TA TA TA TA TA
1 TA TA TA TA TA TA
107968 AACTATATAG
Statistics
Matches: 104, Mismatches: 18, Indels: 32
0.68 0.12 0.21
Matches are distributed among these distances:
1 5 0.05
2 85 0.82
3 14 0.13
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:107986 original size:20 final size:20
Alignment explanation
Indices: 107961--108005 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
107951 ATATATATAT
*
107961 ATATATAAACTATATAGTTC
1 ATATATAAACTACATAGTTC
** *
107981 ATATATGCACTACATAGTTT
1 ATATATAAACTACATAGTTC
108001 ATATA
1 ATATA
108006 CAATATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (20 bp):
ATATATAAACTACATAGTTC
Found at i:108012 original size:47 final size:48
Alignment explanation
Indices: 107892--108022 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 48
107882 ATATATACTA
* *
107892 ATAAACTATATAGTTTATATATACTA-ATAAACTATATAGTTTATTAAT
1 ATAAACTATATAGTTTATATA-AATATATAAACTATATAGTTCATTAAT
* *
107940 ATAAACTATATA-TATATATATATATATAAACTATATAGTTCA-T-AT
1 ATAAACTATATAGTTTATATAAATATATAAACTATATAGTTCATTAAT
** *
107985 ATGCACTACATAGTTTATATACAATATATAAAACTATA
1 ATAAACTATATAGTTTATATA-AATATAT-AAACTATA
108023 AATATAAACT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
45 11 0.16
46 10 0.14
47 29 0.41
48 20 0.29
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (48 bp):
ATAAACTATATAGTTTATATAAATATATAAACTATATAGTTCATTAAT
Found at i:110132 original size:18 final size:18
Alignment explanation
Indices: 110109--110156 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
110099 TCTTTCTGAT
* *
110109 GTCAACATTTCCGGCTAA
1 GTCAACATCTACGGCTAA
110127 GTCAACATCTACGGCTAA
1 GTCAACATCTACGGCTAA
110145 GTCAACATCTAC
1 GTCAACATCTAC
110157 ATAGCCTGTC
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:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (18 bp):
GTCAACATCTACGGCTAA
Found at i:118278 original size:23 final size:23
Alignment explanation
Indices: 118244--118329 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
118234 ACATATTATA
*
118244 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
118267 TGGCACTTCGGTGCATCTTTATACG
1 TGGCACTTCGGTGCA--ATTCTACG
*
118292 -GTC-CTTCGG-GACAAATTCTACG
1 TGGCACTTCGGTG-C-AATTCTACG
*
118314 TGGCACTTCGATGCAA
1 TGGCACTTCGGTGCAA
118330 ATTTATATGA
Statistics
Matches: 48, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
22 7 0.15
23 25 0.52
24 9 0.19
25 7 0.15
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:118933 original size:21 final size:22
Alignment explanation
Indices: 118892--118936 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
118882 TGTAGCAGTA
118892 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAATCGATTCC
* *
118914 CTGTAGTAGGGTAA-CGATTCC
1 CTGTAGCAGGGGAATCGATTCC
118935 CT
1 CT
118937 ATTTGCATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGATTCC
Found at i:125453 original size:24 final size:24
Alignment explanation
Indices: 125375--125463 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 24
125365 GACATATATA
*
125375 TGGCACTACGGTGC-AATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
*
125398 TGGCACTTCGGTGC--ATCTCTACA
1 TGGCACTTCGGTGCAAAT-TCTACG
*
125421 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
125445 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
125464 TATATGAGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.06
23 28 0.52
24 20 0.37
25 3 0.06
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:126057 original size:21 final size:22
Alignment explanation
Indices: 126017--126057 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
126007 GTAGTAGTAT
*
126017 TGTAGCAGGGGAATCGATTCTC
1 TGTAGCAGGGGAACCGATTCTC
*
126039 TGTAGCA-GGGTACCGATTC
1 TGTAGCAGGGGAACCGATTC
126058 CCTATTTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (22 bp):
TGTAGCAGGGGAACCGATTCTC
Found at i:126387 original size:14 final size:14
Alignment explanation
Indices: 126346--126388 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
126336 CAAATTATAT
* *
126346 GTTCGTTTATGTTT
1 GTTCATTTATGTTC
126360 GTTCATTTATGTTC
1 GTTCATTTATGTTC
126374 GTTCATTTATGTTC
1 GTTCATTTATGTTC
126388 G
1 G
126389 AATAGAGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:126677 original size:14 final size:13
Alignment explanation
Indices: 126641--126678 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
126631 TTTTTTTTGG
126641 TGTTGTTCGTTTA
1 TGTTGTTCGTTTA
126654 T-TGTGTTCGTTTA
1 TGT-TGTTCGTTTA
126667 TGTTCGTTCGTT
1 TGTT-GTTCGTT
126679 CGTGTTCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 13 0.59
14 8 0.36
ACGTcount: A:0.05, C:0.11, G:0.24, T:0.61
Consensus pattern (13 bp):
TGTTGTTCGTTTA
Found at i:133816 original size:3 final size:3
Alignment explanation
Indices: 133808--133832 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
133798 TCAGCCAAAG
133808 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
133833 AAAAAAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:134801 original size:14 final size:14
Alignment explanation
Indices: 134779--134810 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
134769 CGTTGGGCAT
134779 CCGAAGGCATCCGA
1 CCGAAGGCATCCGA
*
134793 CCGAGGGCATCCGA
1 CCGAAGGCATCCGA
134807 CCGA
1 CCGA
134811 TGCCATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.38, G:0.31, T:0.06
Consensus pattern (14 bp):
CCGAAGGCATCCGA
Found at i:134949 original size:29 final size:29
Alignment explanation
Indices: 134872--134949 Score: 147
Period size: 29 Copynumber: 2.7 Consensus size: 29
134862 GAGGAGCAGG
*
134872 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTATAAGGTCGCC
134901 AGGAGTGCATGGCGACCTATAAGGTCGCC
1 AGGAGTGCATGGCGACCTATAAGGTCGCC
134930 AGGAGTGCATGGCGACCTAT
1 AGGAGTGCATGGCGACCTAT
134950 GCTGGGAAGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.17
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTATAAGGTCGCC
Found at i:141033 original size:49 final size:49
Alignment explanation
Indices: 140980--141266 Score: 256
Period size: 49 Copynumber: 5.9 Consensus size: 49
140970 ATTTTTCATC
* * * *
140980 TAACTTGCATTAGTGGCACCTTTCTGCTAACAATGCACCGTTAGGTATT
1 TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACCATTAGGTATT
** * * ** *
141029 TAACTTGCATTAGTGGTACCTTTCTGCCAAAAAATACACAATT-TTTCATC
1 TAACTTGCATTAGTGACACCTTTCTG-CAAAAAATGCACCATTAGGT-ATT
* * * *
141079 TAACTTGCATTAG-GGCACTTTTCTGCAAAAAATGCATCATTAGGCATT
1 TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACCATTAGGTATT
* ** *
141127 TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACTATT-TTTCATC
1 TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACCATTAGGT-ATT
* * * * * * *
141176 TAACTTGCATTAATGACACTTTTCTACCAAAAATGCATCGTTAGGCATT
1 TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACCATTAGGTATT
* * * *
141225 TAGCTTACATTAGTGATACCTTTCTGCCAAAAATGCACCATT
1 TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACCATT
141267 TTTCATTATA
Statistics
Matches: 187, Mismatches: 45, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
48 28 0.15
49 133 0.71
50 26 0.14
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (49 bp):
TAACTTGCATTAGTGACACCTTTCTGCAAAAAATGCACCATTAGGTATT
Found at i:141140 original size:98 final size:98
Alignment explanation
Indices: 140962--141272 Score: 421
Period size: 98 Copynumber: 3.2 Consensus size: 98
140952 TCATGCTGAT
* * * * *
140962 AATGCATC-ATTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCTAACAATGCACCGTTAGGT
1 AATGCA-CAATTTTTCATCTAACTTGCATTAG-GGCACTTTTCTGCAAAAAATGCATCGTTAGGC
*
141026 ATTTAACTTGCATTAGTGGTACCTTTCTGCCAAAA
64 ATTTAACTTGCATTAGTGATACCTTTCTGCCAAAA
* *
141061 AATACACAATTTTTCATCTAACTTGCATTAGGGCACTTTTCTGCAAAAAATGCATCATTAGGCAT
1 AATGCACAATTTTTCATCTAACTTGCATTAGGGCACTTTTCTGCAAAAAATGCATCGTTAGGCAT
*
141126 TTAACTTGCATTAGTGACACCTTTCTG-CAAAA
66 TTAACTTGCATTAGTGATACCTTTCTGCCAAAA
* * * * *
141158 AATGCACTATTTTTCATCTAACTTGCATTAATGACACTTTTCTACCAAAAATGCATCGTTAGGCA
1 AATGCACAATTTTTCATCTAACTTGCATT-AGGGCACTTTTCTGCAAAAAATGCATCGTTAGGCA
* *
141223 TTTAGCTTACATTAGTGATACCTTTCTGCC-AAA
65 TTTAACTTGCATTAGTGATACCTTTCTGCCAAAA
*
141256 AATGCACCATTTTTCAT
1 AATGCACAATTTTTCAT
141273 TATAGAGCAC
Statistics
Matches: 189, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
97 32 0.17
98 128 0.68
99 29 0.15
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.36
Consensus pattern (98 bp):
AATGCACAATTTTTCATCTAACTTGCATTAGGGCACTTTTCTGCAAAAAATGCATCGTTAGGCAT
TTAACTTGCATTAGTGATACCTTTCTGCCAAAA
Found at i:150528 original size:35 final size:35
Alignment explanation
Indices: 150435--150795 Score: 293
Period size: 35 Copynumber: 10.3 Consensus size: 35
150425 CAAATATAGT
* * * **
150435 TTTTGAAAATATATAATATATAGGTTTTGGAAACTTAT
1 TTTTGAAAACATATAATATATA-GTTTT-TAAA-ATGG
* * *
150473 TTTTAAAAACGTATAATATATAGTTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
* **
150508 TTTTGAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
* *
150543 TTTTGAAAACATATAATGTATAGTTTTTAAAAAATAG
1 TTTTGAAAACATATAATATATAGTTTTT--AAAATGG
** *
150580 TTTTGAAAATGTATAATATATAGTTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
* * **
150615 TTTTGAAAACATATAGTATATAGTTTTAAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
* * * * *
150650 TTTTGAAAGCGTATAATATATA-TATTTAAAAACGA
1 TTTTGAAAACATATAATATATAGT-TTTTAAAATGG
* * **
150685 TTTTGAAAACATATAGTATA-ATTTTTTAAAA-AA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
* **
150718 TTTTGAAAATATATAATATAT--TTTTCGAAATGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
* * *
150751 TTTTGAAAACGTATAATATATGGTTTTTTAAA-GG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATGG
*
150785 ATTTTCAAAAC
1 -TTTTGAAAAC
150796 GTATGTTTTA
Statistics
Matches: 264, Mismatches: 50, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
32 7 0.03
33 38 0.14
34 11 0.04
35 150 0.57
36 3 0.01
37 36 0.14
38 19 0.07
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAATGG
Found at i:150605 original size:107 final size:106
Alignment explanation
Indices: 150435--150778 Score: 385
Period size: 107 Copynumber: 3.3 Consensus size: 106
150425 CAAATATAGT
* ** ** *
150435 TTTTGAAAATATATAATATATAGGTTTTGGAAACTTATTTTTAAAAACGTATAATATATAGTTTT
1 TTTTGAAAACATATAATATATA-GTTTTTAAAAAATA-TTTTGAAAACGTATAATATATAGTTTT
150500 TAAAACGGTTTTGAAAACATATAGTATATAGTTTTTAAAATAA
64 TAAAACGGTTTTGAAAACATATAGTATATAGTTTTTAAAATAA
* *
150543 TTTTGAAAACATATAATGTATAGTTTTTAAAAAATAGTTTTGAAAATGTATAATATATAGTTTTT
1 TTTTGAAAACATATAATATATAGTTTTTAAAAAATA-TTTTGAAAACGTATAATATATAGTTTTT
*
150608 AAAACGGTTTTGAAAACATATAGTATATAGTTTTAAAAATAA
65 AAAACGGTTTTGAAAACATATAGTATATAGTTTTTAAAATAA
* * * ** * * *
150650 TTTTGAAAGCGTATAATATATA-TATTTAAAAACGATTTTGAAAACATATAGTATA-ATTTTTTA
1 TTTTGAAAACATATAATATATAGTTTTTAAAAAATATTTTGAAAACGTATAATATATAGTTTTTA
** * * **
150713 AAA-AATTTTGAAAATATATA--ATATA-TTTTTCGAAATGG
66 AAACGGTTTTGAAAACATATAGTATATAGTTTTT-AAAATAA
* *
150751 TTTTGAAAACGTATAATATATGGTTTTT
1 TTTTGAAAACATATAATATATAGTTTTT
150779 TAAAGGATTT
Statistics
Matches: 204, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
100 4 0.02
101 29 0.14
102 4 0.02
103 14 0.07
104 10 0.05
105 17 0.08
106 10 0.05
107 96 0.47
108 20 0.10
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.42
Consensus pattern (106 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAAAATATTTTGAAAACGTATAATATATAGTTTTTA
AAACGGTTTTGAAAACATATAGTATATAGTTTTTAAAATAA
Found at i:150868 original size:13 final size:12
Alignment explanation
Indices: 150852--150899 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
150842 TTATTACATA
150852 TTATTATTTTATT
1 TTATT-TTTTATT
150865 TTATTTATTTATT
1 TTATTT-TTTATT
*
150878 TCATTTTTTATTT
1 TTATTTTTTA-TT
150891 TTATTTTTT
1 TTATTTTTT
150900 CGGTCAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 5 0.16
13 26 0.84
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:150876 original size:18 final size:18
Alignment explanation
Indices: 150855--150897 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
150845 TTACATATTA
150855 TTATTTTATTTTATT-TAT
1 TTATTTTATTTT-TTATAT
* *
150873 TTATTTCATTTTTTATTT
1 TTATTTTATTTTTTATAT
150891 TTATTTT
1 TTATTTT
150898 TTCGGTCAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (18 bp):
TTATTTTATTTTTTATAT
Found at i:152080 original size:18 final size:17
Alignment explanation
Indices: 152057--152117 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 17
152047 CATTTAAACC
152057 CTTTTAATTTAAAGTTTT
1 CTTTTAATTTAAA-TTTT
* *
152075 CTTTTACTTTATATTTT
1 CTTTTAATTTAAATTTT
152092 C--TTAATTT-AATTTT
1 CTTTTAATTTAAATTTT
* *
152106 GTTTTACTTTAA
1 CTTTTAATTTAA
152118 TAATTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
16 6 0.18
17 6 0.18
18 11 0.32
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (17 bp):
CTTTTAATTTAAATTTT
Found at i:152480 original size:2 final size:2
Alignment explanation
Indices: 152473--152498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
152463 CGGTTACGAC
152473 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
152499 GAGTTTATTA
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:153876 original size:20 final size:21
Alignment explanation
Indices: 153830--153880 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
153820 TTTTTTTTAC
153830 TTTTTATTAACTTTAAAAAATA
1 TTTTT-TTAACTTTAAAAAATA
153852 TTTTTTTAACTTTAAAAAATA
1 TTTTTTTAACTTTAAAAAATA
153873 TTTTTTTA
1 TTTTTTTA
153881 GCAATATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 24 0.83
22 5 0.17
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTTTAACTTTAAAAAATA
Found at i:154033 original size:76 final size:76
Alignment explanation
Indices: 153948--154104 Score: 221
Period size: 74 Copynumber: 2.1 Consensus size: 76
153938 CTTATCTTTA
153948 AAAATTATATATCACTCCTAGTCCATTTTAAACCACTCTTAACAT-AAA-TTTAAAAATAAATTT
1 AAAATTATATATCACTCCTAGTCCATTTTAAACCACTCTTAACATAAAATTTTAAAAAT-AATTT
*
154011 TAAATTTAAGAT
65 TAAAGTTAAGAT
* * * * *
154023 AAAA-TATATATCACTCTTATTCCATTTTAATCCACTCTTAAGATAAAATTTTAAAAATATTTTT
1 AAAATTATATATCACTCCTAGTCCATTTTAAACCACTCTTAACATAAAATTTTAAAAATAATTTT
*
154087 TAAGTTAAGAT
66 AAAGTTAAGAT
154098 AAAATTA
1 AAAATTA
154105 AAAAAAGAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
74 36 0.50
75 25 0.35
76 11 0.15
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (76 bp):
AAAATTATATATCACTCCTAGTCCATTTTAAACCACTCTTAACATAAAATTTTAAAAATAATTTT
AAAGTTAAGAT
Found at i:159945 original size:14 final size:15
Alignment explanation
Indices: 159926--159964 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
159916 TATTTTAAAT
159926 ATTTTAAAAA-ATAA
1 ATTTTAAAAATATAA
*
159940 ATTTTATAAAATATAT
1 ATTTTA-AAAATATAA
159956 ATTTTAAAA
1 ATTTTAAAA
159965 CTATTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTAAAAATATAA
Found at i:160569 original size:16 final size:15
Alignment explanation
Indices: 160539--160568 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
160529 GATTTTTAGG
160539 AATTTAGTTTTTTTT
1 AATTTAGTTTTTTTT
160554 AATTTAGTTTTTTTT
1 AATTTAGTTTTTTTT
160569 TTGGAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
AATTTAGTTTTTTTT
Found at i:167211 original size:22 final size:22
Alignment explanation
Indices: 167168--167211 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
167158 ATCATTATAT
*
167168 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCAATTATACG
* *
167190 GGCACTTCGGTGCAGTTATACG
1 GGCACTACGGTGCAATTATACG
167212 AGCTGTGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTACGGTGCAATTATACG
Found at i:173601 original size:64 final size:64
Alignment explanation
Indices: 173532--173688 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
173522 TAATGAAGGT
* * **
173532 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTT-TATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCAATGTTTATATT-TTAAAAG
173595 A
64 A
* * *
173596 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCAATGTTTATATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCAATGTTTATATTTTAAAAGA
* * *
173660 GTTCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
173689 ACACCTTTAA
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
63 1 0.01
64 70 0.91
65 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCAATGTTTATATTTTAAAAGA
Found at i:177582 original size:8 final size:8
Alignment explanation
Indices: 177569--177724 Score: 99
Period size: 8 Copynumber: 18.9 Consensus size: 8
177559 TTGAAGAAGA
177569 AAAAAATG
1 AAAAAATG
177577 AAAAAATTG
1 AAAAAA-TG
177586 -AAAAATG
1 AAAAAATG
177593 AAAAAAT-
1 AAAAAATG
*
177600 AAAAAAGG
1 AAAAAATG
*
177608 AAAAGGAAAAG
1 -AAA--AAATG
*
177619 GAAAAATGAG
1 AAAAAAT--G
177629 AAAAAAAATG
1 --AAAAAATG
**
177639 AAAATTTG
1 AAAAAATG
**
177647 TGAAAAT-
1 AAAAAATG
177654 AAAAAATG
1 AAAAAATG
177662 AAAAAATG
1 AAAAAATG
177670 AAAAAATG
1 AAAAAATG
177678 -AAAAATG
1 AAAAAATG
*
177685 AAGAAA-G
1 AAAAAATG
177692 AAAAAA-G
1 AAAAAATG
177699 AGAAAAATG
1 A-AAAAATG
177708 AAAAAATAG
1 AAAAAAT-G
177717 AGAAAAAT
1 A-AAAAAT
177725 AAAGGGGGGG
Statistics
Matches: 117, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
7 28 0.24
8 60 0.51
9 9 0.08
10 10 0.09
11 4 0.03
12 6 0.05
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:177673 original size:6 final size:7
Alignment explanation
Indices: 177570--177712 Score: 80
Period size: 7 Copynumber: 19.7 Consensus size: 7
177560 TGAAGAAGAA
177570 AAAAATG
1 AAAAATG
177577 AAAAAATTG
1 -AAAAA-TG
177586 AAAAATG
1 AAAAATG
177593 AAAAAAT-
1 -AAAAATG
*
177600 AAAAAAG
1 AAAAATG
*
177607 GAAAA-G
1 AAAAATG
* *
177613 GAAAAGG
1 AAAAATG
177620 AAAAATG
1 AAAAATG
*
177627 AGAAA--
1 AAAAATG
177632 AAAAATG
1 AAAAATG
*
177639 AAAATTTG
1 AAAA-ATG
* *
177647 TGAAAATA
1 -AAAAATG
177655 AAAAATG
1 AAAAATG
177662 AAAAAATG
1 -AAAAATG
177670 AAAAAATG
1 -AAAAATG
177678 AAAAATG
1 AAAAATG
177685 AAGAAA-G
1 AA-AAATG
*
177692 AAAAAAGAG
1 -AAAAA-TG
177701 AAAAATG
1 AAAAATG
177708 AAAAA
1 AAAAA
177713 ATAGAGAAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 27
0.73 0.09 0.18
Matches are distributed among these distances:
5 4 0.04
6 11 0.10
7 44 0.40
8 44 0.40
9 6 0.06
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:178797 original size:16 final size:17
Alignment explanation
Indices: 178760--178794 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
178750 AGGTTTCCCA
178760 AAGATATTTGAAGATTG
1 AAGATATTTGAAGATTG
178777 AAGATA-TTGAAGCATTG
1 AAGATATTTGAAG-ATTG
178794 A
1 A
178795 GATGAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (17 bp):
AAGATATTTGAAGATTG
Found at i:179232 original size:55 final size:55
Alignment explanation
Indices: 179101--179520 Score: 383
Period size: 55 Copynumber: 7.7 Consensus size: 55
179091 TTTATGAAGA
* * *
179101 TCGAGTTTTATACTCTCTGATGTAATAGAGAGCGGACCCATTTGTTGAAGA----
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGTTGAAGATTGT
* * * *
179152 TCGAGTTCTATACTCTCTGATGGAATAGAGAGCGAACCCGTTTGTTGAAGATTAT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGTTGAAGATTGT
* *
179207 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGTTGAAGATTGT
* * * * * **
179262 TCGAG-TCTTATACTCCCTGAATGAATAGGGACCGGACACATTTACTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGTTGAAGATTGT
* *
179317 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAAATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGT-TGAAGATTGT
** * * * * *
179372 TTAAGTTCTATACTCCCTGAATGAATATG-GAGTGGACTCATTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATA-GAGAGCGGACCCATTTGTTGAAGATTGT
* * * * * * ** *
179427 TCGAG-TCTTATACTCCCTGAATGAATAGGGAGTGGACACGTTTGCCGAATATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGTTGAAGATTGT
* * *
179482 TCGAG-TCTTATACTC-CTTGAAAGAATAGGGAGCAGACCC
1 TCGAGTTC-TATACTCTC-TGAAGGAATAGAGAGCGGACCC
179521 GTCATTTGAA
Statistics
Matches: 312, Mismatches: 45, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
51 47 0.15
54 6 0.02
55 255 0.82
56 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTGTTGAAGATTGT
Found at i:179327 original size:110 final size:110
Alignment explanation
Indices: 179101--179514 Score: 450
Period size: 110 Copynumber: 3.8 Consensus size: 110
179091 TTTATGAAGA
* * * *
179101 TCGAGTTTTATACTCTCTGATGTAATAGAGAGCGGACCCATTTGTTGAAGA----TCGAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
* * * * * * *
179162 TACTCTCTG-ATGGAATAGAGAGCGAACCCGTTTGTTGAAGATTAT
66 TACTCCCTGAAT-GAATAGGGAGCGGACACATTTATTGAAGATTGT
*
179207 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTTGTTGAAGATTGTTCGAG-TCTT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTC-T
* *
179271 ATACTCCCTGAATGAATAGGGACCGGACACATTTACTGAAGATTGT
65 ATACTCCCTGAATGAATAGGGAGCGGACACATTTATTGAAGATTGT
* **
179317 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAAATTGTTTAAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTCGAGTTCT
* * *
179381 ATACTCCCTGAATGAATATGGAGTGGACTCATTTATTGAAGATTGT
65 ATACTCCCTGAATGAATAGGGAGCGGACACATTTATTGAAGATTGT
* * * * * ** *
179427 TCGAG-TCTTATACTCCCTGAATGAATAGGGAGTGGACACGTTTGCCGAATATTGTTCGAG-TCT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTC-
* *
179490 TATACTCCTTGAAAGAATAGGGAGC
64 TATACTCCCTGAATGAATAGGGAGC
179515 AGACCCGTCA
Statistics
Matches: 260, Mismatches: 37, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
106 46 0.18
109 7 0.03
110 203 0.78
111 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (110 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
TACTCCCTGAATGAATAGGGAGCGGACACATTTATTGAAGATTGT
Found at i:179331 original size:165 final size:165
Alignment explanation
Indices: 179152--179522 Score: 473
Period size: 165 Copynumber: 2.2 Consensus size: 165
179142 TTGTTGAAGA
* * *
179152 TCGAGTTCTATACTCTCTGATGGAATAGAGAGCGAACCCGTTTGT-TGAAGATTATTCGAGTTCT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTT-TATGAAAATTATTCAAGTTCT
* * *
179216 ATACTCTCTGAAGGAATA-GAGAGCAGACCCGTTTGTTGAAGATTGTTCGAGTCTTATACTCCCT
65 ATACTCCCTGAAGGAATATG-GAGCAGACCCATTTATTGAAGATTGTTCGAGTCTTATACTCCCT
*
179280 GAATGAATAGGGACCGGACACATTTACTGAAGATTGT
129 GAATGAATAGGGACCGGACACATTTACCGAAGATTGT
* * *
179317 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAAATTGTTTAAGTTCTA
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAAATTATTCAAGTTCTA
* ** *
179382 TACTCCCTGAATGAATATGGAGTGGACTCATTTATTGAAGATTGTTCGAGTCTTATACTCCCTGA
66 TACTCCCTGAAGGAATATGGAGCAGACCCATTTATTGAAGATTGTTCGAGTCTTATACTCCCTGA
** * * *
179447 ATGAATAGGGAGTGGACACGTTTGCCGAATATTGT
131 ATGAATAGGGACCGGACACATTTACCGAAGATTGT
* *
179482 TCGAG-TCTTATACTC-CTTGAAAGAATAGGGAGC-AGACCCGT
1 TCGAGTTC-TATACTCTC-TGAAGGAATAGAGAGCGA-ACCCGT
179523 CATTTGAAGA
Statistics
Matches: 179, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
164 4 0.02
165 174 0.97
166 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (165 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAAATTATTCAAGTTCTA
TACTCCCTGAAGGAATATGGAGCAGACCCATTTATTGAAGATTGTTCGAGTCTTATACTCCCTGA
ATGAATAGGGACCGGACACATTTACCGAAGATTGT
Found at i:193078 original size:28 final size:28
Alignment explanation
Indices: 193047--193105 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
193037 GTGCTCGCAC
*
193047 TGAAGAGTTGAAGCAGCAGGGAGGATGT
1 TGAAGAGTTGAAACAGCAGGGAGGATGT
193075 TGAAGAGTTGAAACAGCAGGGAGGATGT
1 TGAAGAGTTGAAACAGCAGGGAGGATGT
193103 TGA
1 TGA
193106 GCATATTCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.41, T:0.19
Consensus pattern (28 bp):
TGAAGAGTTGAAACAGCAGGGAGGATGT
Found at i:198106 original size:60 final size:60
Alignment explanation
Indices: 197993--198106 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
197983 CTATAAGATA
** * * **
197993 TTATTTTATTGAGTTTATTGACTATTAAAAGTTATAAAATAGTCTTTTGATTATAAGGAG
1 TTATTTTATTGAGTCCATTGACTATTAAAAGTTACAAAATAGTCATTCAATTATAAGGAG
* *
198053 TTATTTTGTTGAGTCCATTGACTATTAAAAGTTAC-AAATTGATCATTCAATTAT
1 TTATTTTATTGAGTCCATTGACTATTAAAAGTTACAAAATAG-TCATTCAATTAT
198107 TTATTATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (60 bp):
TTATTTTATTGAGTCCATTGACTATTAAAAGTTACAAAATAGTCATTCAATTATAAGGAG
Found at i:199960 original size:14 final size:14
Alignment explanation
Indices: 199918--199961 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
199908 ATCCAATAGC
199918 TTTTAAATATATATT
1 TTTTAAA-ATATATT
* *
199933 TTATAAAATTTATT
1 TTTTAAAATATATT
*
199947 TTTTAAAAAATATT
1 TTTTAAAATATATT
199961 T
1 T
199962 AAAATAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAATATATT
Found at i:220934 original size:3 final size:3
Alignment explanation
Indices: 220926--220960 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
220916 TATTTTAATT
220926 TTA TTA TTA TTA TTA TTA TTA -TA TGTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
220961 GTTTCATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:221160 original size:23 final size:23
Alignment explanation
Indices: 221129--221182 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
221119 CTATTTGTCA
221129 AACCCTAAATAGATTAGGGTTTC
1 AACCCTAAATAGATTAGGGTTTC
*
221152 AACCTTAAATAGATTAGGGTTTC
1 AACCCTAAATAGATTAGGGTTTC
221175 AACCCTAA
1 AACCCTAA
221183 TCCCCTAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (23 bp):
AACCCTAAATAGATTAGGGTTTC
Found at i:222693 original size:14 final size:14
Alignment explanation
Indices: 222674--222700 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
222664 GTACATATTT
222674 ATTTATGTATTTTA
1 ATTTATGTATTTTA
222688 ATTTATGTATTTT
1 ATTTATGTATTTT
222701 TTTATTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
ATTTATGTATTTTA
Found at i:225253 original size:20 final size:20
Alignment explanation
Indices: 225221--225258 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
225211 TTCACCCCAC
*
225221 AAGCTTCCAAGCCGCTAAGT
1 AAGCTTCCAAGCCACTAAGT
225241 AAGCTTCTC-AGCCACTAA
1 AAGCTTC-CAAGCCACTAA
225259 AGCGATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
AAGCTTCCAAGCCACTAAGT
Found at i:227614 original size:18 final size:18
Alignment explanation
Indices: 227564--227606 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
227554 AAAGATATTA
* *
227564 AAAT-AATAAAAGTGATT
1 AAATAAATAAAAATAATT
227581 AAATAAATAAAAATAATT
1 AAATAAATAAAAATAATT
227599 AAAGTAAA
1 AAA-TAAA
227607 AATAATAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
AAATAAATAAAAATAATT
Found at i:229308 original size:14 final size:14
Alignment explanation
Indices: 229290--229327 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
229280 TTTTCCATTT
*
229290 TTTTTCTTTCATGTC
1 TTTTTCTTTC-TCTC
229305 TTTTT-TTTCTCTC
1 TTTTTCTTTCTCTC
229318 TTTTTCTTTC
1 TTTTTCTTTC
229328 GAACAACTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTCTC
Found at i:235624 original size:36 final size:37
Alignment explanation
Indices: 235527--235631 Score: 131
Period size: 36 Copynumber: 2.8 Consensus size: 37
235517 TGAGAATTTT
* *
235527 AAAACAAATTTTTGTCTCACTTGAGATAATTTTTCTCA
1 AAAACAAA-TTTTGTCTCACTTGAGACAATTTCTCTCA
* * **
235565 AAAACAATTTTTATCTCGTTTGAGACAATTTCTCT-A
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTCTCA
*
235601 AAAACAAATGTTGTCTCACTTGAGACAATTT
1 AAAACAAATTTTGTCTCACTTGAGACAATTT
235632 TCCAAATTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 27 0.48
37 22 0.39
38 7 0.12
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (37 bp):
AAAACAAATTTTGTCTCACTTGAGACAATTTCTCTCA
Found at i:235891 original size:26 final size:26
Alignment explanation
Indices: 235835--235891 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
235825 ATTTTGTCTC
*
235835 TTTTGAGAAAGTTCTTTTGAAAGAAT
1 TTTTGAGAAAGTTCTTTGGAAAGAAT
* * *
235861 CTTTGAGTATGTTCTTTGGAACA-AAT
1 TTTTGAGAAAGTTCTTTGGAA-AGAAT
235887 TTTTG
1 TTTTG
235892 TCTCTTTTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (26 bp):
TTTTGAGAAAGTTCTTTGGAAAGAAT
Found at i:235891 original size:61 final size:62
Alignment explanation
Indices: 235796--235964 Score: 182
Period size: 61 Copynumber: 2.7 Consensus size: 62
235786 AAATGAAAAA
* *
235796 AATCTTTGAGTATGTTTCTTGATAACAAAATTTTGTCTCTTTTGAGAA-AGTTCTTTTGAAAG
1 AATCTTTGAGTATGTTTCTTGAGAACAAAATTTTGTCTCTTTTGA-AACAGTCCTTTTGAAAG
* *
235858 AATCTTTGAGTATG-TTCTTTG-GAACAAATTTTTGTCTCTTTTGAAACAGTCCTTTTGAAGAAA
1 AATCTTTGAGTATGTTTC-TTGAGAACAAAATTTTGTCTCTTTTGAAACAGTCCTTTTG-A-AAG
* * * * **
235921 AATCTTTAAGTCTGTTTTTATGAAAACAAAGGTTTGTCTCTTTT
1 AATCTTTGAGTATGTTTCT-TGAGAACAAAATTTTGTCTCTTTT
235965 AAGACAATTC
Statistics
Matches: 90, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
60 2 0.02
61 33 0.37
62 18 0.20
63 15 0.17
64 4 0.04
65 18 0.20
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (62 bp):
AATCTTTGAGTATGTTTCTTGAGAACAAAATTTTGTCTCTTTTGAAACAGTCCTTTTGAAAG
Found at i:236017 original size:30 final size:29
Alignment explanation
Indices: 235972--236087 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 29
235962 TTTAAGACAA
*
235972 TTCCTCTTAAAA-AAACATCTTTGAGATTGT
1 TTCC-CTTAAAACAAAAATCTTTGAG-TTGT
*
236002 TTCCCTT-AAACAAAACCTATCTTTGAGTTTAT
1 TTCCCTTAAAACAAAA---ATCTTTGAG-TTGT
* * *
236034 TTCTCTTAAAACAAAAGTCTGTGAGTTGT
1 TTCCCTTAAAACAAAAATCTTTGAGTTGT
** * *
236063 TTCTTTTGAAATAAAAATCTTTGAG
1 TTCCCTTAAAACAAAAATCTTTGAG
236088 CCTGTTTCTT
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.04
29 29 0.42
30 11 0.16
32 18 0.26
33 8 0.12
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (29 bp):
TTCCCTTAAAACAAAAATCTTTGAGTTGT
Found at i:236025 original size:32 final size:30
Alignment explanation
Indices: 235972--236049 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 30
235962 TTTAAGACAA
*
235972 TTCCTCTTAAA-AAAACATCTTTGAGATTGT
1 TTCC-CTTAAACAAAACATCTTTGAGATTAT
*
236002 TTCCCTTAAACAAAACCTATCTTTGAGTTTAT
1 TTCCCTTAAACAAAA-C-ATCTTTGAGATTAT
*
236034 TTCTCTTAAAACAAAA
1 TTCCCTT-AAACAAAA
236050 GTCTGTGAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.15
30 8 0.20
31 1 0.02
32 18 0.44
33 8 0.20
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.38
Consensus pattern (30 bp):
TTCCCTTAAACAAAACATCTTTGAGATTAT
Found at i:236150 original size:91 final size:92
Alignment explanation
Indices: 236046--236258 Score: 268
Period size: 91 Copynumber: 2.3 Consensus size: 92
236036 CTCTTAAAAC
* * *
236046 AAAAGTCTGTGAGTTGTTTCTTTTGAAATAAAAATCTTTGAGCCTGTTTCTTTTGAACCAAAGTT
1 AAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGCCTGTTTCTTTTGAA-CAAAGTT
*
236111 TTGTTTCTCTTAAGACA-ATTTCGTGA-
65 TTGTCTCTCTTAAGACAGATTTCGTGAG
** * **
236137 AAAAATCTTTGAGTCATTTCTTTTGAAACCAAAATCTTTGAGTTTGTTTCTTTTGAACAAAGTTT
1 AAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGCCTGTTTCTTTTGAACAAAGTTT
* * *
236202 TGTCTCTCTTGAGACAGTTTTTCTTGAG
66 TGTCTCTCTTAAGACAG-ATTTCGTGAG
*
236230 AAAAATCTTTGAGTCTGTTCCTTTTGAAA
1 AAAAATCTTTGAGT-TGTTTCTTTTGAAA
236259 ATCTTTGAGA
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
90 22 0.21
91 49 0.48
92 7 0.07
93 14 0.14
94 11 0.11
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (92 bp):
AAAAATCTTTGAGTTGTTTCTTTTGAAACAAAAATCTTTGAGCCTGTTTCTTTTGAACAAAGTTT
TGTCTCTCTTAAGACAGATTTCGTGAG
Found at i:236548 original size:179 final size:169
Alignment explanation
Indices: 236217--236564 Score: 597
Period size: 179 Copynumber: 2.0 Consensus size: 169
236207 CTCTTGAGAC
236217 AGTTTTTCTTGAGAAAAATCTTTGAGTCTGTTCCTTTTGAAAATCTTTGAGATTGTGTATCTTAA
1 AGTTTTTCTTGAGAAAAATCTTTGAGTCTGTTCCTTTTGAAAATCTTTGAGATTGTGTATCTTAA
236282 CAAAATCATGTGATTCTATTTCTTTAAAAACGAATTTCTTGAGATAATTTTAATAAAAACCAACC
66 CAAAATCATGTGATTCTATTTCTTTAAAAACGAATTTCTTGAGATAATTTTAATAAAAACCAACC
236347 TTTGGGATTGTTTCTTTTTAGAAAAATCCTTGAGTCTGT
131 TTTGGGATTGTTTCTTTTTAGAAAAATCCTTGAGTCTGT
*
236386 AGTTTTTCTTGAGAAAAATCTTTGAGTCTGTTCCTTTTGAAAAATCTTTGAGATTGTGTCTCTTA
1 AGTTTTTCTTGAGAAAAATCTTTGAGTCTGTTCCTTTTG-AAAATCTTTGAGATTGTGTATCTTA
236451 ACAAAATCATATGTGATTCTATTTCTTTAAAAACGAATTTTATCTCTTGAGATAATTTTTAATAA
65 ACAAAATC--ATGTGATTCTATTTCTTTAAAAACGAA---T-T-TCTTGAGATAA-TTTTAAT-A
236516 AAAACCAACCTTTGGGATTGTTTCTTTTTAGAAAAATCCTTGAGTCTGT
121 AAAACCAACCTTTGGGATTGTTTCTTTTTAGAAAAATCCTTGAGTCTGT
236565 TTCTTTGGAA
Statistics
Matches: 168, Mismatches: 1, Indels: 10
0.94 0.01 0.06
Matches are distributed among these distances:
169 39 0.23
170 32 0.19
172 27 0.16
175 1 0.01
176 1 0.01
177 11 0.07
178 7 0.04
179 50 0.30
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (169 bp):
AGTTTTTCTTGAGAAAAATCTTTGAGTCTGTTCCTTTTGAAAATCTTTGAGATTGTGTATCTTAA
CAAAATCATGTGATTCTATTTCTTTAAAAACGAATTTCTTGAGATAATTTTAATAAAAACCAACC
TTTGGGATTGTTTCTTTTTAGAAAAATCCTTGAGTCTGT
Found at i:236889 original size:134 final size:133
Alignment explanation
Indices: 236649--237030 Score: 491
Period size: 134 Copynumber: 2.8 Consensus size: 133
236639 AATCGTTATC
* * *
236649 CCTAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTGTCATCTCCTGACCCGATCTCTCCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCTCCCGACCAGATCTCT-CAT
* * *
236714 CGCGTAGGAGCCATGTCACCCTTAGATAACCAGACGTCCTCATCACATAGGAACCGTATTATCGC
65 CGCGTAGGAGCCGTGTCACCCTTAGATAACCAGACGTCCTCATCACATAGGAACCGGATTATCAC
236779 CCTT
130 CCTT
*
236783 CCTAAAGATGGCCAGAACTCTTTATCACGTATGAGCCGTGTCATCTCCCGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCTCCCGACCAGATCT-CTCAT
* * *
236848 CGCGTAGGAGCCGTGTCACCCCTAGATAACCA-ACCGTCCTCATCACGTAGGAACCGGGTTATCA
65 CGCGTAGGAGCCGTGTCACCCTTAGATAACCAGA-CGTCCTCATCACATAGGAACCGGATTATCA
236912 CCCTT
129 CCCTT
* * ** * *
236917 CCTAAAGATGGCCAAGAACTCTTCATCATGCATGAGTAGTGTCATC-CCTCGATCAGATTTCTCA
1 CCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCATCTCC-CGACCAGATCTCTCA
* * * * * *
236981 TCACGTAAGAACCGTGTCACCCTTAGATGACCCGAAC-TCTTCATCACATA
64 TCGCGTAGGAGCCGTGTCACCCTTAGATAACCAG-ACGTCCTCATCACATA
237031 TGAGCAGTGT
Statistics
Matches: 217, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
133 1 0.00
134 176 0.81
135 39 0.18
136 1 0.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.25
Consensus pattern (133 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCTCCCGACCAGATCTCTCATC
GCGTAGGAGCCGTGTCACCCTTAGATAACCAGACGTCCTCATCACATAGGAACCGGATTATCACC
CTT
Found at i:237216 original size:3 final size:3
Alignment explanation
Indices: 237208--237248 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
237198 TATTTTAATT
237208 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TGTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
237249 GTTTCATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:248021 original size:78 final size:78
Alignment explanation
Indices: 247892--248048 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
247882 TTTTGATATA
*
247892 CTATTTAAATGTTAAAATTATTTTTAAAATTATAATTAAGTTAAAATAACGTGTAAATATTGAGG
1 CTATTTAAATGTTAAAATTAATTTTAAAATTATAATTAAGTTAAAATAACGTGTAAATATTGAGG
247957 AAAAAACTATTAC
66 AAAAAACTATTAC
247970 CTATTTAAATGTTAAAATTAATTTTAAAATTATAATTAAGTTAAAATAACGTGTAAATATTGAGG
1 CTATTTAAATGTTAAAATTAATTTTAAAATTATAATTAAGTTAAAATAACGTGTAAATATTGAGG
248035 AAAAAACTATTAC
66 AAAAAACTATTAC
248048 C
1 C
248049 ATACAAATTA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.38
Consensus pattern (78 bp):
CTATTTAAATGTTAAAATTAATTTTAAAATTATAATTAAGTTAAAATAACGTGTAAATATTGAGG
AAAAAACTATTAC
Found at i:255753 original size:81 final size:81
Alignment explanation
Indices: 255653--256217 Score: 731
Period size: 81 Copynumber: 7.0 Consensus size: 81
255643 CTATTTTAAA
*
255653 TAAAAGATTAATTGTCTAGCTGTGCATTTGACATAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAGTGTCAATTATGCCAGTTAGATGAAAG
* *
255718 GTTAAATACCTTTGAG
66 GCTAAATGCCTTTGAG
* *
255734 TAAAATATTAATTGCCTAGCTGTGCATTTGACATAAAGGTGTTC-ATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAGTG-TCAATTATGCCAGTTAGATGAAA
* *
255798 GGTTAAATACCTTTGAG
65 GGCTAAATGCCTTTGAG
* *
255815 TAAAAGATTAATTGCCTAGCTGTGCATTTGACA-GAAAGATATCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAG-TGTCAATTATGCCAGTTAGATGAAA
* *
255879 GGTTAAATACCTTTGAG
65 GGCTAAATGCCTTTGAG
* * * *
255896 TAAAAAATTAATTGTCTAGCTGTGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAGTGTCAATTATGCCAGTTAGATGAAAG
* *
255961 ACTAAATGGCTTTGAG
66 GCTAAATGCCTTTGAG
* * * * * * * * * * *
255977 TTAAAGATTAAATGGCTAGTTGTGTAATTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAGTGTCAATTATGCCAGTTAGATGAAAG
256042 GCTAAATGCCTTTGAG
66 GCTAAATGCCTTTGAG
* *
256058 TAAAAGATTAATTGCCTAGCTGTGTATTTGACA-AAAATGTGTCAATTATGCTAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAA-GTGTCAATTATGCCAGTTAGATGAAA
*
256122 GGATAAATGCCTTTGAG
65 GGCTAAATGCCTTTGAG
* * * * * * *
256139 TTAAAGATTAAATGCCTAGTTGTGCAATTGACATAAATGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAGTGTCAATTATGCCAGTTAGATGAAAG
*
256204 CCTAAATGCCTTTG
66 GCTAAATGCCTTTG
256218 GGAATGCTTA
Statistics
Matches: 428, Mismatches: 50, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
80 8 0.02
81 411 0.96
82 9 0.02
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACATAAAAGTGTCAATTATGCCAGTTAGATGAAAG
GCTAAATGCCTTTGAG
Found at i:269958 original size:81 final size:81
Alignment explanation
Indices: 269829--270348 Score: 621
Period size: 81 Copynumber: 6.4 Consensus size: 81
269819 CTGTTTTAAA
* *
269829 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAATTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
269894 GTTAAATATCTTTAAG
66 GTTAAATACCTTTGAG
*
269910 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTTC-ATTATGCCAGTTAAATGAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTG-TCAATTATGCCAGTTAGATGAAA
269974 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * *
269991 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTATCAATTATGTCAGTTAGATGAAAA
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
270056 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
270072 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAATGTGTCAATTATGCCGGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
270137 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
270153 TAAAAGATTAAATGCCTAGATGTGCAATTGGCATAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
270218 GCTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* * * * ** ** * ** *
270234 TTAAAGATTAAATGACTAGTTGTAAAATAGGA-TGAAAGGTGTCAAACATGCAAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGCTGT-GCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* * *
270298 GGCTAAATGCCTTTGGG
65 GGTTAAATACCTTTGAG
* * * * *
270315 TAAAAGACTAAATGCTTAACAGTGCATTTTGACA
1 TAAAAGATTAATTGCCTAGCTGTGCA-TTTGACA
270349 TAAAACAGTG
Statistics
Matches: 381, Mismatches: 53, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
80 3 0.01
81 374 0.98
82 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:278666 original size:3 final size:3
Alignment explanation
Indices: 278647--278690 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
278637 ATATATATAC
* *
278647 ATT ATTT ATT GTT ATT ATT AATT ATT ATT ATT ATT ATT AAT ATT
1 ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
278691 TTTAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:278671 original size:16 final size:16
Alignment explanation
Indices: 278647--278682 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
278637 ATATATATAC
* *
278647 ATTATTTATTGTTATT
1 ATTAATTATTATTATT
278663 ATTAATTATTATTATT
1 ATTAATTATTATTATT
278679 ATTA
1 ATTA
278683 TTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTAATTATTATTATT
Found at i:278695 original size:9 final size:9
Alignment explanation
Indices: 278659--278702 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
278649 TATTTATTGT
278659 TATTATTAA
1 TATTATTAA
*
278668 TTATTATTAT
1 -TATTATTAA
278678 TATTATTAA
1 TATTATTAA
*
278687 TATTTTTAA
1 TATTATTAA
*
278696 TTTTATT
1 TATTATT
278703 TTTTGTAGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTATTAA
Found at i:281795 original size:26 final size:26
Alignment explanation
Indices: 281766--281820 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
281756 ACATATTGTG
*
281766 CATT-TTGTTATTTTTCTTTACATTCA
1 CATTATTGTTACTTTT-TTTACATTCA
* *
281792 CATTATTTTTCCTTTTTTTACATTCA
1 CATTATTGTTACTTTTTTTACATTCA
281818 CAT
1 CAT
281821 GTCTCATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.60
Consensus pattern (26 bp):
CATTATTGTTACTTTTTTTACATTCA
Found at i:284052 original size:94 final size:94
Alignment explanation
Indices: 283940--284623 Score: 897
Period size: 94 Copynumber: 7.1 Consensus size: 94
283930 AATTTCAGAG
283940 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
284005 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
284034 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
284099 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
*
284128 CCAA-TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
284192 GGGACCGCTGGTTGTCAATAAAAAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
*
284221 CCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
284286 GGGACCGCTGGTTGTCAATAAACAATTTC
66 GGGACCGCTGGTTGTCAATAAACAATTTC
* * ** * * * *
284315 CCAAGTTCAACTTCACAGCGAAGGATATTGGACTAAAGACAGCTCAAGCTCAACTTCACGAAGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* ** ***
284380 GGG-GCGACTGACTGTCAACTTCCCAATTTC
66 GGGACCG-CTGGTTGTCAA-TAAACAATTTC
* * * * * *
284410 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGG
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* ** *
284475 CGAAAGGG-CGGCTGACTGTCAACAAACAACTTCTCAATTTC
62 CG-AAGGGACCGCTGGTTGTC-A-ATA-AA-----CAATTTC
*
284516 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
284581 CGAAGGGACCGCTGGTTGTCAATAAACAAATTTT
62 CGAAGGGACCGCTGGTTGTCAATAAAC-AATTTC
*
284615 CCAGTTTCA
1 CCAATTTCA
284624 GAGTCAACTT
Statistics
Matches: 531, Mismatches: 41, Indels: 35
0.87 0.07 0.06
Matches are distributed among these distances:
93 93 0.18
94 253 0.48
95 16 0.03
98 1 0.00
99 72 0.14
100 7 0.01
101 1 0.00
103 2 0.00
104 2 0.00
105 6 0.01
106 78 0.15
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (94 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:284171 original size:187 final size:188
Alignment explanation
Indices: 283940--284623 Score: 881
Period size: 187 Copynumber: 3.5 Consensus size: 188
283930 AATTTCAGAG
*
283940 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAA
*
284005 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
284070 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
131 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
284128 CCAA-TTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAA
* *
284192 GGGACCGCTGGTTGTCAATAAAAAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCT
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
284257 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
131 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
* * * * * * *
284315 CCAAGTTCAACTTCACAGCGAAGGATATTGGACT-AAAGACAGCTCAAGCTCAACTTCACGAAGA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAA-ACAACGCAAGTTCAACTTCACGACGA
* ** *** *
284379 AGGG-GCGACTGACTGTCAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
65 AGGGACCG-CTGGTTGTCAA-TAAACAATTTC----CCAATTTCAACTTCACAACGAAGGATATT
* * * * * ** *
284443 GGACTCAAGACAGCACAAGCTCAACTTCACGGCGAAAGGG-CGGCTGACTGTCAACAAACAACTT
124 GGACTCAAGACAACGCAAGTTCAACTTCACGACG-AAGGGACCGCTGGTTGTC-A-ATA-AA---
284507 CTCAATTTC
182 --CAATTTC
* *
284516 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGA
* *
284581 CGAAGGGACCGCTGGTTGTCAATAAACAAATTTTCCAGTTTCA
62 CGAAGGGACCGCTGGTTGTCAATAAAC-AATTTCCCAATTTCA
284624 GAGTCAACTT
Statistics
Matches: 430, Mismatches: 42, Indels: 35
0.85 0.08 0.07
Matches are distributed among these distances:
187 188 0.44
188 67 0.16
189 7 0.02
193 66 0.15
194 6 0.01
195 2 0.00
196 2 0.00
201 15 0.03
204 2 0.00
205 72 0.17
206 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (188 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:284546 original size:106 final size:105
Alignment explanation
Indices: 284221--284656 Score: 408
Period size: 106 Copynumber: 4.3 Consensus size: 105
284211 AAAAAATTTC
* * * * *
284221 CCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACG-A
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGACGAA
* ** *
284285 AGGGACCGCTGGTTGTC-AATA-AA-----CAATTTC----
66 AGGG-CGGCTGACTGTCAAAAACAACTTCTCAATTTCAGAG
* * * *
284315 CCAAGTTCAACTTCACAGCGAAGGATATTGGACTAAAGACAGCTCAAGCTCAACTTCACGAAGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGACGAA
* * *
284380 GGGGCGACTGACTGT------CAACTTCCCAATTTCAGAG
66 AGGGCGGCTGACTGTCAAAAACAACTTCTCAATTTCAGAG
*
284414 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGGCGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGACGAA
284479 AGGGCGGCTGACTGTCAACAAACAACTTCTCAATTTCAGAG
66 AGGGCGGCTGACTGTCAA-AAACAACTTCTCAATTTCAGAG
* * * *
284520 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACG-A
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGACGAA
* ** * * *
284584 AGGGACCGCTGGTTGTCAATAAACAAATTTTCCAGTTTCAGAG
66 AGGG-CGGCTGACTGTCAA-AAACAACTTCT-CAATTTCAGAG
* * *
284627 TCAACTTCAACTTCAC-GTCGAAAGATATTG
1 CCAATTTCAACTTCACAG-CGAAGGATATTG
284657 ACCTCATAAT
Statistics
Matches: 284, Mismatches: 37, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
90 2 0.01
94 62 0.22
95 11 0.04
99 73 0.26
105 5 0.02
106 96 0.34
107 35 0.12
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACGACGAA
AGGGCGGCTGACTGTCAAAAACAACTTCTCAATTTCAGAG
Found at i:284920 original size:3 final size:3
Alignment explanation
Indices: 284901--284944 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
284891 ATATATATAC
*
284901 ATT ATTT ATT GTT ATT ATT AATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
284945 TTTTAATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:284925 original size:16 final size:16
Alignment explanation
Indices: 284901--284957 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
284891 ATATATATAC
* *
284901 ATTATTTATTGTTATT
1 ATTAATTATTATTATT
284917 ATTAATTATTATTATT
1 ATTAATTATTATTATT
284933 ATT-ATTATTATT-TT
1 ATTAATTATTATTATT
284947 -TTAATT-TTATT
1 ATTAATTATTATT
284958 TTTTGTAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
13 7 0.18
14 5 0.13
15 9 0.24
16 17 0.45
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTAATTATTATTATT
Found at i:291343 original size:37 final size:37
Alignment explanation
Indices: 291270--291344 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
291260 GTTGAAAAAT
** *
291270 ATTTATATATTTTTTTAAAAAAATTTGAATTCATAAA
1 ATTTATATATTTTTTTAAAAAAATTAAAAATCATAAA
* *
291307 ATTTATATAATTTTTTTTAGAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTTTTAAAAAAATTAAAAATCATAAA
291344 A
1 A
291345 AATGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTTTTAAAAAAATTAAAAATCATAAA
Found at i:292665 original size:13 final size:13
Alignment explanation
Indices: 292649--292706 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
292639 ATAATAAAAT
292649 ATTAATTATGATA
1 ATTAATTATGATA
292662 ATTAAATTA--ATA
1 ATT-AATTATGATA
* *
292674 AATATATT-TAATA
1 ATTA-ATTATGATA
292687 TATTAATTATGATA
1 -ATTAATTATGATA
292701 ATTAAT
1 ATTAAT
292707 ATACTTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
11 1 0.03
12 8 0.22
13 15 0.42
14 12 0.33
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (13 bp):
ATTAATTATGATA
Found at i:292705 original size:21 final size:21
Alignment explanation
Indices: 292639--292709 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
292629 TTTAAATGTT
*
292639 ATAA-TAAAATATTAATTATG
1 ATAATTAATATATTAATTATG
*
292659 ATAATT-A-A-ATTAATAAAT-
1 ATAATTAATATATTAAT-TATG
*
292677 ATATTTAATATATTAATTATG
1 ATAATTAATATATTAATTATG
292698 ATAATTAATATA
1 ATAATTAATATA
292710 CTTTATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 11 0.27
19 4 0.10
20 8 0.20
21 18 0.44
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
ATAATTAATATATTAATTATG
Found at i:292726 original size:14 final size:15
Alignment explanation
Indices: 292705--292816 Score: 69
Period size: 14 Copynumber: 7.9 Consensus size: 15
292695 ATGATAATTA
292705 ATATACTTTATATTT
1 ATATACTTTATATTT
292720 A-ATAC-TTATATTT
1 ATATACTTTATATTT
*
292733 ATATACTTTAATACTT
1 ATATACTTT-ATATTT
*** *
292749 ATAT-CCAAACACTTT
1 ATATACTTTATA-TTT
*
292764 -TTTACTTTATA-TT
1 ATATACTTTATATTT
*
292777 ATATACTTTATATAT
1 ATATACTTTATATTT
* *
292792 ATATA-TATATA-CT
1 ATATACTTTATATTT
292805 -TATACTTTATAT
1 ATATACTTTATAT
292817 ATGTATGTAA
Statistics
Matches: 72, Mismatches: 16, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
12 4 0.06
13 17 0.24
14 27 0.38
15 15 0.21
16 9 0.12
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:292742 original size:22 final size:22
Alignment explanation
Indices: 292713--292805 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 22
292703 TAATATACTT
292713 TATA-TTTAATACTTATATTTA
1 TATACTTTAATACTTATATTTA
**
292734 TATACTTTAATACTTATATCCA
1 TATACTTTAATACTTATATTTA
* * **
292756 AACACTTTTTTACTT-TATATTA
1 TATACTTTAATACTTATAT-TTA
*
292778 TATACTTT-ATA-TATATATATA
1 TATACTTTAATACT-TATATTTA
292799 TATACTT
1 TATACTT
292806 ATACTTTATA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.02
21 19 0.34
22 36 0.64
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TATACTTTAATACTTATATTTA
Found at i:293259 original size:20 final size:20
Alignment explanation
Indices: 293222--293272 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
293212 AAATTAAATA
293222 TATATATATATATAATGAATG
1 TATATATA-ATATAATGAATG
*
293243 T-TATGATAATATGATGAATG
1 TATAT-ATAATATAATGAATG
293263 TATATATAAT
1 TATATATAAT
293273 GTACATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (20 bp):
TATATATAATATAATGAATG
Found at i:293883 original size:25 final size:24
Alignment explanation
Indices: 293835--293880 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
293825 TAATAAGGGA
293835 TGAAATTGAATTAATTATAAAATG
1 TGAAATTGAATTAATTATAAAATG
*
293859 TGAAGTTGATATTAA-TATAAAA
1 TGAAATTGA-ATTAATTATAAAA
293881 ATGGACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (24 bp):
TGAAATTGAATTAATTATAAAATG
Found at i:294062 original size:13 final size:14
Alignment explanation
Indices: 294037--294069 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
294027 ACTAAATTGA
294037 ACAAATATAAAATT
1 ACAAATATAAAATT
294051 ACAAAT-TAAAATT
1 ACAAATATAAAATT
294064 A-AAATA
1 ACAAATA
294070 CAATAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 8 0.44
14 6 0.33
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATATAAAATT
Found at i:302543 original size:22 final size:22
Alignment explanation
Indices: 302518--302563 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
302508 AATGTACTTC
302518 GATGGGGCATCCAATGCATTAG
1 GATGGGGCATCCAATGCATTAG
302540 GATGGGGCATCCAATGCATTAG
1 GATGGGGCATCCAATGCATTAG
302562 GA
1 GA
302564 CATGGCATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (22 bp):
GATGGGGCATCCAATGCATTAG
Found at i:302570 original size:22 final size:22
Alignment explanation
Indices: 302522--302572 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
302512 TACTTCGATG
**
302522 GGGCATCCAATGCATTAGGATG
1 GGGCATCCAATGCATTAGGACA
302544 GGGCATCCAATGCATTAGGACA
1 GGGCATCCAATGCATTAGGACA
*
302566 TGGCATC
1 GGGCATC
302573 GGGGCAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (22 bp):
GGGCATCCAATGCATTAGGACA
Found at i:304136 original size:22 final size:22
Alignment explanation
Indices: 304105--304165 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
304095 TTGGTGCAGA
304105 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * * *
304127 GGGAACCGATTCCCCCCTGTAG
1 GGGAATCGATACCCCCTTGAAG
304149 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
304166 GGAGGTTCTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:307524 original size:13 final size:13
Alignment explanation
Indices: 307508--307533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307498 AACTATAAAG
307508 TATATATATATAA
1 TATATATATATAA
307521 TATATATATATAA
1 TATATATATATAA
307534 ACTATAAGGT
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):
TATATATATATAA
Found at i:307548 original size:58 final size:54
Alignment explanation
Indices: 307485--307631 Score: 150
Period size: 58 Copynumber: 2.6 Consensus size: 54
307475 AAGTATAGTA
*
307485 TATATAAAGTGTAAACTATAAAGTATATATATATAATATATATATATAAACTATAAGG
1 TATATAAAGTATAAACTATAAAGTATATATATAT-ATATA-A-ATATAAACTATAA-G
* * * * * * *
307543 TATATATACTTTAAAGTATAAAGTGTATATATATATATAACTATAAAGTATAAG
1 TATATAAAGTATAAACTATAAAGTATATATATATATATAAATATAAACTATAAG
307597 TATATTATAAGTATATAAACTATAAAGTATATATA
1 TATA-TA-AAG--TATAAACTATAAAGTATATATA
307632 CTTATACTAA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
54 5 0.07
55 13 0.18
56 2 0.03
57 5 0.07
58 48 0.66
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.38
Consensus pattern (54 bp):
TATATAAAGTATAAACTATAAAGTATATATATATATATAAATATAAACTATAAG
Found at i:307562 original size:23 final size:24
Alignment explanation
Indices: 307542--307591 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
307532 AAACTATAAG
* *
307542 GTATATATACTTTAAAGTATAAAGT
1 GTATATATA-TATAAACTATAAAGT
307567 GTATATATATATATAACTATAAAGT
1 GTATATATATATA-AACTATAAAGT
307592 ATAAGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (24 bp):
GTATATATATATAAACTATAAAGT
Found at i:307593 original size:32 final size:34
Alignment explanation
Indices: 307536--307627 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 34
307526 ATATATAAAC
* * *
307536 TATAAGGTATATATACTTTAAAGTATAAAGTGTA-
1 TATAA-GTATATAAACTATAAAGTATAAAGTATAT
307570 TAT-A-TATATATAACTATAAAGTAT-AAGTATAT
1 TATAAGTATATA-AACTATAAAGTATAAAGTATAT
307602 TATAAGTATATAAACTATAAAGTATA
1 TATAAGTATATAAACTATAAAGTATA
307628 TATACTTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 12 0.24
32 14 0.28
33 15 0.30
34 9 0.18
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (34 bp):
TATAAGTATATAAACTATAAAGTATAAAGTATAT
Found at i:307629 original size:81 final size:80
Alignment explanation
Indices: 307498--307693 Score: 249
Period size: 79 Copynumber: 2.4 Consensus size: 80
307488 ATAAAGTGTA
* *
307498 AACTATAAAGTATATATATATAATATATATATATAAACTATAAGGTATATATACTTTAAAGTATA
1 AACTATAAAGTATATATATAT-ATATATATATATAAACTATAAAGTATATATAC-TTAAACTA-A
*
307563 AAGTGTATATATATATAT
63 AACTGTATATATATATAT
*
307581 AACTATAAAGTATA-AGTATAT-TATA-AGTATATAAACTATAAAGTATATATACTTATACTAAA
1 AACTATAAAGTATATA-TATATATATATA-TATATAAACTATAAAGTATATATACTTAAACTAAA
*
307643 ACTTTATATATATATAT
64 ACTGTATATATATATAT
*
307660 ATA-TATATA-TATATATATATATATATATATATAA
1 A-ACTATAAAGTATATATATATATATATATATATAA
307694 GTTAAGTATA
Statistics
Matches: 101, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
78 9 0.09
79 35 0.35
80 9 0.09
81 28 0.28
82 1 0.01
83 19 0.19
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (80 bp):
AACTATAAAGTATATATATATATATATATATATAAACTATAAAGTATATATACTTAAACTAAAAC
TGTATATATATATAT
Found at i:307637 original size:32 final size:32
Alignment explanation
Indices: 307527--307637 Score: 97
Period size: 32 Copynumber: 3.4 Consensus size: 32
307517 ATAATATATA
* * *
307527 TATATAAAC-TATAAGGTATATATACTTTAAAG
1 TATATATACTTATAA-GTATATAAACTATAAAG
*
307559 TATA-A-AGTGTATATA-TATATATAACTATAAAG
1 TATATATACT-TATA-AGTATATA-AACTATAAAG
307591 TATAAGTATA-TTATAAGTATATAAACTATAAAG
1 TAT-A-TATACTTATAAGTATATAAACTATAAAG
307624 TATATATACTTATA
1 TATATATACTTATA
307638 CTAAAACTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
30 1 0.02
31 11 0.17
32 25 0.38
33 16 0.24
34 10 0.15
35 2 0.03
36 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.39
Consensus pattern (32 bp):
TATATATACTTATAAGTATATAAACTATAAAG
Found at i:307654 original size:2 final size:2
Alignment explanation
Indices: 307647--308247 Score: 202
Period size: 2 Copynumber: 302.5 Consensus size: 2
307637 ACTAAAACTT
307647 TA TA TA TA TA TA 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 TA TA TA TA TA TA
307689 TA TA -A GT- TA -A GTA TA TA TA TA TA TA TA T- TA TA GT- TA TA
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
307727 TA TA TA CT- TT TA CTT TA TA GTT TA TA TA CA TA TA T- TA CA TA
1 TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
307768 CT- TA TA CTT TA TA T- TG TA TG 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 TA TA TA TA TA TA
* *
307810 TA TA TA TA TA TA TA T- TG T- TA TA TA TA TA CT- TA TA TA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* * * *
307851 TA TT TA AA CTA TA TA AA CTA TA TA -A T- TA TA CA TA GTA TA TA
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
307892 T- TA TA -A T- TA TA CA TA -A TA TA TA TA -A GTG TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * *
307930 -A CTA GT- TA TA TG TA GT- TCA -A TA GT- TCA TA TA -A AA CTC TA
1 TA -TA -TA TA TA TA TA -TA T-A TA TA -TA T-A TA TA TA TA -TA TA
* * * * *
307969 TA GTT TA TA CA TGG TA TA TA TA GTT TA TA CA TA TA TA TA -A TA
1 TA -TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
308011 TA TA TA TA TA TA TA T- TA T- TA TA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
308049 TA TA TA T- TT TA TA -A TA TA TA TA TA CTT TA TA T- TA CA CTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA
* * * * *
308090 TA TA TA CA CTA TA TA GTT TA TA T- TA -A TA AA CTA TA CA GTT TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
308132 TA TA TA T- TA TA TA CGA TA TA TA CTT TA TA TA TA CA CTA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
** * * * * *
308174 GC T- TA TA TA GTT TA TA T- TA -A TA AA CTA TA TGG TT TA TA CA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA
308214 TA -A 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 TA TA T
308248 TATTTAATTG
Statistics
Matches: 443, Mismatches: 81, Indels: 150
0.66 0.12 0.22
Matches are distributed among these distances:
1 40 0.09
2 372 0.84
3 31 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:308171 original size:29 final size:29
Alignment explanation
Indices: 308130--308190 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
308120 CTATACAGTT
* *
308130 TATATATATTATATA-CGATATATACTTTA
1 TATATACACTATATAGC-ATATATACTTTA
* *
308159 TATATACACTATATAGCTTATATAGTTTA
1 TATATACACTATATAGCATATATACTTTA
308188 TAT
1 TAT
308191 TAATAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (29 bp):
TATATACACTATATAGCATATATACTTTA
Done.