Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002656.1 Hibiscus syriacus cultivar Beakdansim tig00005432_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: 60113
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:1362 original size:45 final size:45
Alignment explanation
Indices: 1260--1363 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 45
1250 TATCATCCCA
*
1260 TCATGCTTATAATACACCATGATACCATTTCCATTATGGCATACTT
1 TCATGCTT-TTATACACCATGATACCATTTCCATTATGGCATACTT
* * * *
1306 TCATGTTTTTATACACTATTATA-CATTT-CATTTATGGCATCCTT
1 TCATGCTTTTATACACCATGATACCATTTCCA-TTATGGCATACTT
1350 TCATGCCTTTTATA
1 TCATG-CTTTTATA
1364 TTCTTACGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.04
44 22 0.44
45 19 0.38
46 7 0.14
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (45 bp):
TCATGCTTTTATACACCATGATACCATTTCCATTATGGCATACTT
Found at i:2890 original size:17 final size:16
Alignment explanation
Indices: 2868--2914 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
2858 ATTTGTTCCA
2868 AAGGACCACTATGTCCC-
1 AAGGACCACTA--TCCCG
2885 AAGGACCACTATCCCG
1 AAGGACCACTATCCCG
2901 AAGGACCACATATC
1 AAGGACCAC-TATC
2915 ACATATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.14
16 9 0.32
17 15 0.54
ACGTcount: A:0.34, C:0.34, G:0.17, T:0.15
Consensus pattern (16 bp):
AAGGACCACTATCCCG
Found at i:2955 original size:44 final size:41
Alignment explanation
Indices: 2881--2977 Score: 140
Period size: 44 Copynumber: 2.3 Consensus size: 41
2871 GACCACTATG
2881 TCCCAAGGACCACTATCCCGAAGGACCACATATCACATATA
1 TCCCAAGGACCACTATCCCGAAGGACCACATATCACATATA
* *
2922 TCCCGAAGGACCACTATGTCCTGAAGGACCACATATCACATATG
1 TCCC-AAGGACCACTA--TCCCGAAGGACCACATATCACATATA
2966 TCCCAAAGGACC
1 TCCC-AAGGACC
2978 GCTCCTTAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
41 4 0.08
42 11 0.22
44 35 0.70
ACGTcount: A:0.34, C:0.33, G:0.15, T:0.18
Consensus pattern (41 bp):
TCCCAAGGACCACTATCCCGAAGGACCACATATCACATATA
Found at i:3372 original size:23 final size:23
Alignment explanation
Indices: 3327--3374 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3317 ATGTCATGTT
*
3327 TAATAACATATATCATATGTATA
1 TAATAACATATATCATATATATA
*
3350 TAATAACTTATATCAT-TCATATA
1 TAATAACATATATCATAT-ATATA
3373 TA
1 TA
3375 GTCACATAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAACATATATCATATATATA
Found at i:5131 original size:34 final size:32
Alignment explanation
Indices: 5071--5140 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5061 CCTTACAAAC
*
5071 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
5103 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
5137 TCCC
1 TCCC
5141 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:8174 original size:18 final size:18
Alignment explanation
Indices: 8148--8202 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
8138 ACTTAGAATT
*
8148 TGTCTCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
8166 TGTCCCGAAGGACCACTA
1 TGTCCCGAATGACCACTA
8184 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
8202 T
1 T
8203 CCCGAAGGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:8690 original size:15 final size:15
Alignment explanation
Indices: 8670--8705 Score: 58
Period size: 13 Copynumber: 2.5 Consensus size: 15
8660 GTTTATATCA
8670 TATTCACACAACATG
1 TATTCACACAACATG
8685 TATT--CACAACATG
1 TATTCACACAACATG
8698 TATTCACA
1 TATTCACA
8706 ACAATCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.31
Consensus pattern (15 bp):
TATTCACACAACATG
Found at i:8694 original size:13 final size:13
Alignment explanation
Indices: 8676--8708 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
8666 ATCATATTCA
8676 CACAACATGTATT
1 CACAACATGTATT
8689 CACAACATGTATT
1 CACAACATGTATT
8702 CACAACA
1 CACAACA
8709 ATCATATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.24
Consensus pattern (13 bp):
CACAACATGTATT
Found at i:9163 original size:21 final size:22
Alignment explanation
Indices: 9137--9210 Score: 102
Period size: 21 Copynumber: 3.5 Consensus size: 22
9127 AAGTTCCCCG
9137 GGTATCGATATCCTACA-CATA-
1 GGTATCGATA-CCTACATCATAT
9158 GGTATCGATACC-ACATCATAT
1 GGTATCGATACCTACATCATAT
*
9179 GGTATCGATA-CTTCATCATAT
1 GGTATCGATACCTACATCATAT
9200 GGTATCGATAC
1 GGTATCGATAC
9211 TTTTCATACA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
19 3 0.06
20 7 0.15
21 38 0.79
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (22 bp):
GGTATCGATACCTACATCATAT
Found at i:9225 original size:21 final size:21
Alignment explanation
Indices: 9152--9231 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
9142 CGATATCCTA
**
9152 CACATAGGTATCGATACCACAT
1 CACAT-GGTATCGATACTTCAT
*
9174 CATATGGTATCGATACTTCAT
1 CACATGGTATCGATACTTCAT
*
9195 CATATGGTATCGATACTTTTCAT
1 CACATGGTATCGATAC--TTCAT
9218 -ACAT-GTATCGATAC
1 CACATGGTATCGATAC
9232 CCTATGCATC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 40 0.77
22 7 0.13
23 5 0.10
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (21 bp):
CACATGGTATCGATACTTCAT
Found at i:10255 original size:79 final size:79
Alignment explanation
Indices: 10145--10499 Score: 559
Period size: 79 Copynumber: 4.5 Consensus size: 79
10135 CATTATTTCA
* * *
10145 TTTCATGTCAATAATGCACCCATATGCATTATTCTGTTATGTCGATAATGTACCCATATACATAT
1 TTTCATGCCACTAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATAT
*
10210 CAGCTAAGGCATCT
66 CAGCTAAGGCATCC
* * *
10224 TTTTATGCCACTAATGCACCCGTATGCATTATTTTGTTATGCCGATAATGTACCCATATACATAT
1 TTTCATGCCACTAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATAT
*
10289 CAGTTAAGGCATCC
66 CAGCTAAGGCATCC
*
10303 TTTCATGCCACTAATGCACCCATATGCATTATTATGTTATGCCGATAATGTACCCATATACATAT
1 TTTCATGCCACTAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATAT
*
10368 CAGCTAAGACATCC
66 CAGCTAAGGCATCC
* * * *
10382 TTTCATGCCACTAATGCACCGATATGCATTATTTTGTTATTCCAATAATGTACCCATATACATAT
1 TTTCATGCCACTAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATAT
10447 CAGCTAAGGCATCC
66 CAGCTAAGGCATCC
* *
10461 -TTCATGCCACTAATTCACCCATATGCATTATTCTTTTAT
1 TTTCATGCCACTAATGCACCCATATGCATTATTCTGTTAT
10500 TCATTAGTTT
Statistics
Matches: 254, Mismatches: 22, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
78 35 0.14
79 219 0.86
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTCATGCCACTAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATAT
CAGCTAAGGCATCC
Found at i:10914 original size:20 final size:20
Alignment explanation
Indices: 10889--10942 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
10879 CAGTATCGAT
10889 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
* *
10909 GTATCGATACTACCCTGCTATG
1 GTATCGATAC--CCCTACCATG
*
10931 ATATCGATACCC
1 GTATCGATACCC
10943 TTTCCAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
22 17 0.59
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:14350 original size:54 final size:54
Alignment explanation
Indices: 14290--14824 Score: 737
Period size: 54 Copynumber: 9.9 Consensus size: 54
14280 TAGTACCCAT
** ** *
14290 ACGGTTATTCATAAACATATTATGAATTTCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * *
14344 ATGGTTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACCTAGTGTTGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * *
14398 ACAGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGAGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* *
14452 ACGGTTATTCATCCACATAGGATGAATCCCGTGAAATGTACACTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * * *
14506 ACGGTTATTCATACACATAGGATGAATTACGTAAAATGTACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * *
14560 ATGGTTATTAATCCACATAAGATGAATTCCGTGAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * ** * *
14614 ACGGTTATTTATCCATATAGGATGAATTTTGTAAAATGCACACTTAGTGCCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * *
14668 ACTGTTATTCATCCACATAGGATGAATTCCGTAAAATGCACATTTAGTGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * * *
14722 ATGGTTATTCATCCACATAGGATGAATTCCGTGAAATACAAACTTAATGTCGAA
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
*
14776 ACGGTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTG
1 ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
14825 CCTATTTGGT
Statistics
Matches: 422, Mismatches: 59, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 422 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (54 bp):
ACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
Found at i:21707 original size:20 final size:20
Alignment explanation
Indices: 21682--21730 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
21672 TTCAATCAGC
*
21682 ATCGATACCGAAGAGGGAG-T
1 ATCGATACCGAAG-GGAAGAT
*
21702 ATCGATACTGAAGGGAAGAT
1 ATCGATACCGAAGGGAAGAT
21722 ATCGATACC
1 ATCGATACC
21731 AGTTTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (20 bp):
ATCGATACCGAAGGGAAGAT
Found at i:22323 original size:34 final size:34
Alignment explanation
Indices: 22285--22423 Score: 152
Period size: 34 Copynumber: 3.8 Consensus size: 34
22275 CTATAACTGA
*
22285 AATGCATATGGGTGCATTATCGGCGTAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
22319 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
22362 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
22398 AATACATATGGGTGCATTATCGGCAT
1 AATGCATATGGGTGCATTATCGGCAT
22424 GAAATGATGC
Statistics
Matches: 90, Mismatches: 4, Indels: 22
0.78 0.03 0.19
Matches are distributed among these distances:
34 49 0.54
35 3 0.03
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.03
45 25 0.28
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:22368 original size:79 final size:79
Alignment explanation
Indices: 22232--22473 Score: 421
Period size: 79 Copynumber: 3.1 Consensus size: 79
22222 TCGAATGAAC
* * *
22232 AAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCTATAACTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
*
22297 TGCATTATCGGCGT
66 TGCATTATCGGCAT
22311 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
22376 TGCATTATCGGCAT
66 TGCATTATCGGCAT
* * *
22390 AAAAGAATAATACATATGGGTGCATTATCGGCATGAAATGATGCCATAGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
22455 TGCATTATCGGCAT
66 TGCATTATCGGCAT
22469 AAAAG
1 AAAAG
22474 TATGCTATAC
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 156 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGG
TGCATTATCGGCAT
Found at i:22370 original size:45 final size:44
Alignment explanation
Indices: 22319--22495 Score: 203
Period size: 45 Copynumber: 4.2 Consensus size: 44
22309 GTAAAAGAAT
*
22319 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATA-CTGA
22364 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A-T--
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATACTGA
* *
22398 AATACATATGGGTGCATTATCGGCATGAAATGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATA-CTGA
* * *
22443 AATGCATATGGGTGCATTATCGGCATAAAAGTATGCTATACTTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAC-TGA
22488 AATGCATA
1 AATGCATA
22496 ATGGTGTATT
Statistics
Matches: 113, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
34 25 0.22
35 3 0.03
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 4 0.04
45 71 0.63
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATACTGA
Found at i:27450 original size:23 final size:23
Alignment explanation
Indices: 27382--27450 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
27372 ACACCTTATA
* * *
27382 TGGCATTTCAGTGCATTTCTAAG
1 TGGCACTTCGGTGCATTTCTACG
* *
27405 TGACACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
27428 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
27451 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:30708 original size:20 final size:20
Alignment explanation
Indices: 30683--30720 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30673 TGATTCAATC
*
30683 AGTATCGATACCGAAGGGGG
1 AGTATCAATACCGAAGGGGG
30703 AGTATCAATACCGAAGGG
1 AGTATCAATACCGAAGGG
30721 AAGGTATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (20 bp):
AGTATCAATACCGAAGGGGG
Found at i:31326 original size:34 final size:34
Alignment explanation
Indices: 31288--31355 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
31278 CTATAGCTTA
31288 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
31322 AATGCATATGGGTGCATTATTGGCATGAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
31356 GCCATAGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:31370 original size:79 final size:77
Alignment explanation
Indices: 31235--31395 Score: 261
Period size: 79 Copynumber: 2.1 Consensus size: 77
31225 ACGAATGAAC
* * *
31235 AAAAGAATAATGCATATTGGTGCATTATTGGCATGAAAGGATGCTATAGCTTAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTTAAATG--TATGGG
31300 TGCATTATCGGCAT
64 TGCATTATCGGCAT
31314 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAG-TTGAAATGTATGGGT
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTT-AAATGTATGGGT
31378 GCATTATCGGCAT
65 GCATTATCGGCAT
31391 AAAAG
1 AAAAG
31396 TATGCTATAC
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
77 25 0.32
78 2 0.03
79 51 0.65
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (77 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAGCTTAAATGTATGGGTG
CATTATCGGCAT
Found at i:31376 original size:43 final size:43
Alignment explanation
Indices: 31328--31413 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
31318 GAATAATGCA
* * *
31328 TATGGGTGCATTATTGGCATGAAAGAATGCCATAGTTGAAATG
1 TATGGGTGCATTATCGGCATAAAAGAATGCCATACTTGAAATG
* *
31371 TATGGGTGCATTATCGGCATAAAAGTATGCTATACTTGAAATG
1 TATGGGTGCATTATCGGCATAAAAGAATGCCATACTTGAAATG
31414 CATAATGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (43 bp):
TATGGGTGCATTATCGGCATAAAAGAATGCCATACTTGAAATG
Found at i:33968 original size:21 final size:22
Alignment explanation
Indices: 33944--33990 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
33934 ATTGTGTAAT
33944 ATTTTTATAAT-TTCTAAAATA
1 ATTTTTATAATATTCTAAAATA
* *
33965 A-TTTTATAATATTTTAGAATA
1 ATTTTTATAATATTCTAAAATA
33986 ATTTT
1 ATTTT
33991 GTAAAACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 9 0.41
21 10 0.45
22 3 0.14
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTTATAATATTCTAAAATA
Found at i:33969 original size:20 final size:21
Alignment explanation
Indices: 33941--33990 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
33931 ATAATTGTGT
*
33941 AATATTTTTATAAT-TTCTAA
1 AATAATTTTATAATATTCTAA
* *
33961 AATAATTTTATAATATTTTAG
1 AATAATTTTATAATATTCTAA
33982 AATAATTTT
1 AATAATTTT
33991 GTAAAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
AATAATTTTATAATATTCTAA
Found at i:34001 original size:21 final size:21
Alignment explanation
Indices: 33961--34001 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33951 TAATTTCTAA
* *
33961 AATAATTTTATAATATTTTAG
1 AATAATTTTATAAAACTTTAG
*
33982 AATAATTTTGTAAAACTTTA
1 AATAATTTTATAAAACTTTA
34002 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
AATAATTTTATAAAACTTTAG
Found at i:34260 original size:23 final size:24
Alignment explanation
Indices: 34215--34260 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
34205 AAAATATTTC
34215 AATGAAATTTCATAATTTTAAAAA
1 AATGAAATTTCATAATTTTAAAAA
* *
34239 AATGATATTT-ATATTTTTAAAA
1 AATGAAATTTCATAATTTTAAAA
34261 GATGAGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
AATGAAATTTCATAATTTTAAAAA
Found at i:34384 original size:17 final size:15
Alignment explanation
Indices: 34361--34404 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
34351 ATTAAAAGGA
34361 TATATTTATATAACTT
1 TATATTTATATAA-TT
*
34377 TAATATTTTTATAATT
1 T-ATATTTATATAATT
34393 TATCATTTATAT
1 TAT-ATTTATAT
34405 TTTTACAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 11 0.46
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTTATATAATT
Found at i:35725 original size:21 final size:20
Alignment explanation
Indices: 35642--35796 Score: 82
Period size: 21 Copynumber: 7.7 Consensus size: 20
35632 AATGACCAAC
**
35642 AAATCGCAACGCGA-AAT-A
1 AAATCGCAACGCGATTTTCA
***
35660 AAATCGCAACGCGATCCCCA
1 AAATCGCAACGCGATTTTCA
* ** *
35680 GAATCGCAAATC-AGTTTCCA
1 AAATCGCAACGCGA-TTTTCA
*
35700 AAATCGCAACGCGATTCTTGA
1 AAATCGCAACGCGATT-TTCA
* * *
35721 AAATCGCAATGCGATAGTACA
1 AAATCGCAACGCGAT-TTTCA
* **
35742 AATTCGCATTGCGATTTTCCA
1 AAATCGCAACGCGATTTT-CA
* * *
35763 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGATTTTCA
35783 AAATCGCAACGCGA
1 AAATCGCAACGCGA
35797 ACACATAAAT
Statistics
Matches: 103, Mismatches: 27, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
18 14 0.14
19 1 0.01
20 41 0.40
21 47 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGATTTTCA
Found at i:35787 original size:20 final size:19
Alignment explanation
Indices: 35762--35957 Score: 130
Period size: 19 Copynumber: 10.6 Consensus size: 19
35752 GCGATTTTCC
35762 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGAA-ATG
*
35782 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAA-ATG
*
35801 ATAAATCGCAACGCGAACA-C
1 A-AAATCGCAACGCGAA-ATG
* *
35821 ATAAATCGCAACGTG-TATCCG
1 A-AAATCGCAACGCGAAAT--G
* *
35842 TATATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
35856 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
35875 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
35894 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
35908 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
35927 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
35946 AAAATCGCAACG
1 AAAATCGCAACG
35958 AGAGAATCGC
Statistics
Matches: 147, Mismatches: 15, Indels: 29
0.77 0.08 0.15
Matches are distributed among these distances:
14 18 0.12
15 1 0.01
16 4 0.03
17 3 0.02
18 4 0.03
19 60 0.41
20 57 0.39
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:35882 original size:19 final size:19
Alignment explanation
Indices: 35858--35955 Score: 152
Period size: 19 Copynumber: 5.4 Consensus size: 19
35848 GCAACGAGAG
35858 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35877 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35896 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
35910 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35929 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35948 AATCGCAA
1 AATCGCAA
35956 CGAGAGAATC
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 56 0.78
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:35966 original size:33 final size:33
Alignment explanation
Indices: 35845--35974 Score: 113
Period size: 33 Copynumber: 3.8 Consensus size: 33
35835 GTATCCGTAT
35845 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * * * *
35878 ATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGA
1 ATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-A
*
35911 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAA
35949 ATCGCAACGAGAGAATCGCAATGCGA
1 ATCGCAACGAGAGAATCGCAATGCGA
35975 TTTTCATTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
31 7 0.09
32 7 0.09
33 33 0.44
34 1 0.01
35 1 0.01
36 2 0.03
38 10 0.13
39 7 0.09
40 7 0.09
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:35993 original size:52 final size:52
Alignment explanation
Indices: 35845--35974 Score: 260
Period size: 52 Copynumber: 2.5 Consensus size: 52
35835 GTATCCGTAT
35845 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
35897 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
35949 ATCGCAACGAGAGAATCGCAATGCGA
1 ATCGCAACGAGAGAATCGCAATGCGA
35975 TTTTCATTTC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (52 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
Found at i:36025 original size:20 final size:19
Alignment explanation
Indices: 35964--36099 Score: 150
Period size: 19 Copynumber: 7.6 Consensus size: 19
35954 AACGAGAGAA
*
35964 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35983 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
35997 TCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36016 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
36036 TCGCATTGCGA-TTTC-TC
1 TCGCATTGCGATTTTCATT
36053 T-G---TGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36068 TCGCATTGCGATTTTCATTT
1 TCGCATTGCGATTTTCA-TT
36088 TCGCATTGCGAT
1 TCGCATTGCGAT
36100 AGTCATTTTG
Statistics
Matches: 99, Mismatches: 5, Indels: 25
0.77 0.04 0.19
Matches are distributed among these distances:
13 5 0.05
14 14 0.14
15 2 0.02
16 5 0.05
17 5 0.05
18 4 0.04
19 32 0.32
20 32 0.32
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:36105 original size:20 final size:20
Alignment explanation
Indices: 36066--36108 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
36056 GCGATTTTCA
**
36066 TTTCGCATTGCGATTTTCAT
1 TTTCGCATTGCGATAGTCAT
36086 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
36106 TTT
1 TTT
36109 GCCTTCAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (20 bp):
TTTCGCATTGCGATAGTCAT
Found at i:36221 original size:14 final size:14
Alignment explanation
Indices: 36202--36238 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36192 CATCAATTAC
36202 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
36216 ACAAATCATCTTTT
1 ACAAATCAACTTTT
36230 ACAAATCAA
1 ACAAATCAA
36239 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:38201 original size:14 final size:14
Alignment explanation
Indices: 38182--38238 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38172 GCGAAATGAA
*
38182 AATCGCAACGACAG
1 AATCGCAACGAAAG
38196 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
38213 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
38229 AATCGCAACG
1 AATCGCAACG
38239 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:38209 original size:33 final size:33
Alignment explanation
Indices: 38163--38255 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38153 GCGAAACCAA
*
38163 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
38196 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
38229 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
38256 TGCGATTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:38220 original size:19 final size:19
Alignment explanation
Indices: 38126--38260 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
38116 TAGTTTACTT
* *
38126 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
38146 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
38165 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38184 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
38198 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
38217 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
38231 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38250 TCGCAATGCGA
1 TCGCAACGCGA
38261 TTTTTATTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:42604 original size:23 final size:26
Alignment explanation
Indices: 42560--42607 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 26
42550 GTGAACATTA
42560 AATAAAAACATTACAAACTAAATAAT
1 AATAAAAACATTACAAACTAAATAAT
*
42586 AATAATAA-ATTA-AAA-TAAATAA
1 AATAAAAACATTACAAACTAAATAA
42608 ATGCAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 3 0.14
25 4 0.19
26 7 0.33
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (26 bp):
AATAAAAACATTACAAACTAAATAAT
Found at i:44522 original size:38 final size:37
Alignment explanation
Indices: 44437--45043 Score: 582
Period size: 38 Copynumber: 15.9 Consensus size: 37
44427 ATTATTTTAG
*
44437 AAAACGATTTTTGAAAATGTATATAT-TATATAGTTTTG
1 AAAAC-ATTTTTGAAAAT-TATATATATATATAGTTTTT
**
44475 AAATTA-TTTTGAAAACTTATATAATATATATAGTTTTT
1 AAAACATTTTTGAAAA-TTATAT-ATATATATAGTTTTT
* *
44513 AAAACA-TTTTGAAAAAATATATATAATATATAATTTTT
1 AAAACATTTTTG-AAAATTATATAT-ATATATAGTTTTT
*
44551 AAAACATTTTTGAAAGCTTATATATAATATATAGTTTTT
1 AAAACATTTTTGAAA-ATTATATAT-ATATATAGTTTTT
44590 AAAACA-TTTTGAAAATATATATATAATATATAGTTTTT
1 AAAACATTTTTGAAAAT-TATATAT-ATATATAGTTTTT
44628 AAAACATTTTTGAAAACTTATATATAATATATAGTTTTT
1 AAAACATTTTTGAAAA-TTATATAT-ATATATAGTTTTT
* *
44667 AAAACA-CTTTGAATATATATATAATATATATAGTTTTT
1 AAAACATTTTTGAAAAT-TATAT-ATATATATAGTTTTT
44705 AAAACATTTTTGAAAACTTATATATAATATATAGTTTTTTT
1 AAAACATTTTTGAAAA-TTATATAT-ATATATAG--TTTTT
* *
44746 TAAACA-TTTT-AAAAATATATATAATATATAGTTTTT
1 AAAACATTTTTGAAAATTATATAT-ATATATAGTTTTT
*
44782 AAAACATTTTGGAAAACTTATATATAATATATAGTTTTT
1 AAAACATTTTTGAAAA-TTATATAT-ATATATAGTTTTT
*
44821 AAAATATTTTTGAAAA-TATATATATTATATAGTTTTT
1 AAAACATTTTTGAAAATTATATATA-TATATAGTTTTT
*
44858 AAAAACATTTTTGAAAA-TATATATATTATATAATTTTT
1 -AAAACATTTTTGAAAATTATATATA-TATATAGTTTTT
*
44896 AAAAATATTTTTGAAAA-TATATAT-TATATAGTTTTTTT
1 -AAAACATTTTTGAAAATTATATATATATATAG--TTTTT
* *
44934 AAAAAAATATTTTTGAAAA-TATATAT-TATTTAGTTTTTT
1 ---AAAACATTTTTGAAAATTATATATATATATAG-TTTTT
* * *
44973 AAAAATTATTTTTGAAAA-TATATAT-TATATGGTTTTG
1 -AAAA-CATTTTTGAAAATTATATATATATATAGTTTTT
* * *
45010 AAAATAATTTTT-AAAA-CATATATAATATGTAGTT
1 AAAA-CATTTTTGAAAATTATATAT-ATATATAGTT
45044 ATAAAAATGA
Statistics
Matches: 506, Mismatches: 34, Indels: 59
0.84 0.06 0.10
Matches are distributed among these distances:
35 10 0.02
36 42 0.08
37 46 0.09
38 224 0.44
39 138 0.27
40 36 0.07
41 10 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
AAAACATTTTTGAAAATTATATATATATATAGTTTTT
Found at i:44587 original size:77 final size:76
Alignment explanation
Indices: 44445--45043 Score: 655
Period size: 77 Copynumber: 7.9 Consensus size: 76
44435 AGAAAACGAT
* * * **
44445 TTTTG-AAAATGTATATATTATATAGTTTTGAAATTA-TTTTGAAAACTTATATA-ATATATATA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATA-ATATATA
44507 GTTTTTAAAACA
65 GTTTTTAAAACA
* *
44519 TTTTGAAAAAATATATATAATATATAATTTTTAAAACATTTTTGAAAGCTTATATATAATATATA
1 TTTTG-AAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATA
44584 GTTTTTAAAACA
65 GTTTTTAAAACA
44596 TTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATA
44661 GTTTTTAAAACA
65 GTTTTTAAAACA
* *
44673 CTTTG-AATATATATATAATATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATAT
1 TTTTGAAAAATATATAT-A-ATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATAT
*
44737 AGTTTTTTTTAAACA
64 AG--TTTTTAAAACA
*
44752 TTTT-AAAAATATATATAATATATAGTTTTTAAAACATTTTGGAAAACTTATATATAATATATAG
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATAG
*
44816 TTTTTAAAATA
66 TTTTTAAAACA
* *
44827 TTTTTG-AAAATATATATATTATATAGTTTTTAAAAACATTTTTGAAAA--TATATATATTATAT
1 -TTTTGAAAAATATATATAATATATAGTTTTT-AAAACATTTTTGAAAACTTATATATAATATAT
* *
44889 AATTTTTAAAAATA
64 AGTTTTT-AAAACA
*
44903 TTTTTG-AAAATATATAT--TATATAGTTTTTTTAAAAAAATATTTTTGAAAA--TATATAT--T
1 -TTTTGAAAAATATATATAATATATAG--TTTTT---AAAACATTTTTGAAAACTTATATATAAT
* *
44961 ATTTAGTTTTTTAAAAATTA
60 ATATAG-TTTTT-AAAA-CA
* * * *
44981 TTTTTG-AAAATATATAT--TATATGGTTTTGAAAATAATTTTT-AAAAC--ATATATAATATGT
1 -TTTTGAAAAATATATATAATATATAGTTTTTAAAA-CATTTTTGAAAACTTATATATAATATAT
45040 AGTT
64 AGTT
45044 ATAAAAATGA
Statistics
Matches: 473, Mismatches: 28, Indels: 48
0.86 0.05 0.09
Matches are distributed among these distances:
73 14 0.03
74 20 0.04
75 42 0.09
76 97 0.21
77 227 0.48
78 50 0.11
79 23 0.05
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (76 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAACTTATATATAATATATAG
TTTTTAAAACA
Found at i:45071 original size:7 final size:7
Alignment explanation
Indices: 45061--45128 Score: 63
Period size: 7 Copynumber: 9.9 Consensus size: 7
45051 TGATTTTGTG
45061 TTTTTTA
1 TTTTTTA
45068 TTTTTTA
1 TTTTTTA
45075 TTTTTTA
1 TTTTTTA
45082 ---TTTA
1 TTTTTTA
45086 TTTTTTA
1 TTTTTTA
**
45093 TTACTTA
1 TTTTTTA
45100 TTTTTTA
1 TTTTTTA
45107 TTTTATT-
1 TTTT-TTA
45114 TTAATTTTA
1 TT--TTTTA
45123 TTTTTT
1 TTTTTT
45129 TTGTTTAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
4 4 0.08
7 38 0.76
8 4 0.08
9 4 0.08
ACGTcount: A:0.18, C:0.01, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:45087 original size:11 final size:10
Alignment explanation
Indices: 45068--45127 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 10
45058 GTGTTTTTTA
45068 TTTTTTATTT
1 TTTTTTATTT
45078 TTTATTTATTT
1 TTT-TTTATTT
* *
45089 TTTATTACTTA
1 TTTTTTA-TTT
45100 TTTTTTATTT
1 TTTTTTATTT
*
45110 TATTTTAATTT
1 T-TTTTTATTT
45121 TATTTTT
1 T-TTTTT
45128 TTTGTTTAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
10 9 0.22
11 32 0.78
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:45093 original size:25 final size:24
Alignment explanation
Indices: 45061--45128 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
45051 TGATTTTGTG
45061 TTTTTTATTTTTTATTTTTTATTT
1 TTTTTTATTTTTTATTTTTTATTT
**
45085 ATTTTTTATTACTTATTTTTTATTT
1 -TTTTTTATTTTTTATTTTTTATTT
* *
45110 TATTTTA-ATTTTATTTTTT
1 TTTTTTATTTTTTATTTTTT
45129 TTGTTTAAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
23 9 0.24
24 6 0.16
25 22 0.59
ACGTcount: A:0.18, C:0.01, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTTTATTTTTTATTTTTTATTT
Found at i:46274 original size:15 final size:15
Alignment explanation
Indices: 46256--46298 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
46246 TTAGTTATTC
*
46256 ATTTTTTCTTTTTTA
1 ATTTTTTCATTTTTA
**
46271 ATTTTAGCATTTTTA
1 ATTTTTTCATTTTTA
*
46286 ATTTTTTTATTTT
1 ATTTTTTCATTTT
46299 AAAATTATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (15 bp):
ATTTTTTCATTTTTA
Found at i:46281 original size:23 final size:23
Alignment explanation
Indices: 46255--46299 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
46245 TTTAGTTATT
**
46255 CATTTTTTCTTTTTTAATTTTAG
1 CATTTTTAATTTTTTAATTTTAG
*
46278 CATTTTTAATTTTTTTATTTTA
1 CATTTTTAATTTTTTAATTTTA
46300 AAATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (23 bp):
CATTTTTAATTTTTTAATTTTAG
Found at i:46393 original size:13 final size:14
Alignment explanation
Indices: 46374--46408 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
46364 TTTTTCTTTG
46374 ATTTATTTAATATT
1 ATTTATTTAATATT
*
46388 -TTTATTTATTATT
1 ATTTATTTAATATT
46401 ATTTATTT
1 ATTTATTT
46409 CATTTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:46416 original size:49 final size:49
Alignment explanation
Indices: 46362--46532 Score: 128
Period size: 49 Copynumber: 3.6 Consensus size: 49
46352 ATAATTTTCC
46362 TTTTTTTCTTTGATTTATTTAATATTTTTATTTATTATTATTTAT-TTCA
1 TTTTTTTCTTT-ATTTATTTAATATTTTTATTTATTATTATTTATATTCA
* ** * * *
46411 TTTTTTCCTTTGATTTGCTTAGT-TTATTTTTTTATTATTATTT-TGTT--
1 TTTTTTTCTTT-ATTTATTTAATATT-TTTATTTATTATTATTTATATTCA
* * *
46458 TTTATGTT-TTTATTTATTT-TTATTTTTATTTATT-TTATTTTATATTTA
1 TTT-TTTTCTTTATTTATTTAATATTTTTATTTATTATTA-TTTATATTCA
* *
46506 -TTTTTTATTT-TTTATTTAACATTTTTA
1 TTTTTTTCTTTATTTATTTAATATTTTTA
46533 ACTTTTTAGA
Statistics
Matches: 97, Mismatches: 15, Indels: 22
0.72 0.11 0.16
Matches are distributed among these distances:
44 3 0.03
45 13 0.13
46 21 0.22
47 18 0.19
48 5 0.05
49 37 0.38
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (49 bp):
TTTTTTTCTTTATTTATTTAATATTTTTATTTATTATTATTTATATTCA
Found at i:46454 original size:11 final size:11
Alignment explanation
Indices: 46434--46521 Score: 62
Period size: 11 Copynumber: 8.2 Consensus size: 11
46424 TTTGCTTAGT
*
46434 TTATTTTTTTA
1 TTATTATTTTA
*
46445 TTATTATTTTG
1 TTATTATTTTA
*
46456 TTTTTATGTTT-
1 TTATTAT-TTTA
46467 TTATTTATTTTTA
1 TTA-TTA-TTTTA
*
46480 TTTTTA-TTTA
1 TTATTATTTTA
46490 TT-TTATTTTA
1 TTATTATTTTA
46500 -TATTTATTTT-
1 TTA-TTATTTTA
46510 TTATT-TTTTA
1 TTATTATTTTA
46520 TT
1 TT
46522 TAACATTTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
9 8 0.13
10 14 0.22
11 26 0.41
12 12 0.19
13 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:46479 original size:6 final size:6
Alignment explanation
Indices: 46439--46522 Score: 64
Period size: 6 Copynumber: 13.5 Consensus size: 6
46429 TTAGTTTATT
* * *
46439 TTTTTA TTATTA -TTTTG TTTTTA TGTTTT- TATTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA TTTTTA TTTTTA TTTTTA
* *
46486 TTTATTT TATTTTA TATTTA TTTTTTA TTTTTTA TTT
1 TTT-TTA T-TTTTA TTTTTA -TTTTTA -TTTTTA TTT
46523 AACATTTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
5 6 0.10
6 32 0.52
7 22 0.35
8 2 0.03
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:46519 original size:25 final size:24
Alignment explanation
Indices: 46433--46522 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 24
46423 ATTTGCTTAG
*
46433 TTTATTTTTTTATTATTATTTTGTT
1 TTTATTTTTTTATT-TTATTTTATT
*
46458 TTTATGTTTTTA-TTTATTTTTATT
1 TTTATTTTTTTATTTTA-TTTTATT
46482 TTTATTTATTTTATTTTATATTTATT
1 TTTATTT-TTTTATTTTAT-TTTATT
46508 TTT-TATTTTTTATTT
1 TTTAT-TTTTTTATTT
46523 AACATTTTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
23 3 0.05
24 13 0.23
25 26 0.46
26 15 0.26
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTATTTTTTTATTTTATTTTATT
Found at i:46532 original size:20 final size:17
Alignment explanation
Indices: 46386--46523 Score: 102
Period size: 18 Copynumber: 7.6 Consensus size: 17
46376 TTATTTAATA
*
46386 TTTTTATTTATTATTAT
1 TTTTTATTTATTTTTAT
*
46403 TTATTTCATTTTTTCCTTTGAT
1 TT-TTT-ATTTATT--TTT-AT
*
46425 TTGCTTAGTTTATTTTT-T
1 TT-TTTA-TTTATTTTTAT
*
46443 TATTATTATTTTGTTTTTAT
1 T-TT-TTA-TTTATTTTTAT
46463 GTTTTTATTTATTTTTA-
1 -TTTTTATTTATTTTTAT
46480 TTTTTATTTA-TTTTAT
1 TTTTTATTTATTTTTAT
*
46496 TTTATATTTATTTTTTAT
1 TTTTTATTTA-TTTTTAT
46514 TTTTTATTTA
1 TTTTTATTTA
46524 ACATTTTTAA
Statistics
Matches: 97, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
15 5 0.05
16 19 0.20
17 2 0.02
18 29 0.30
19 21 0.22
20 6 0.06
21 4 0.04
22 11 0.11
ACGTcount: A:0.18, C:0.03, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTTATTTATTTTTAT
Found at i:47933 original size:18 final size:18
Alignment explanation
Indices: 47910--47945 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47900 ATTTGACATG
47910 TAATATTATATAATTTGA
1 TAATATTATATAATTTGA
47928 TAATATTATATAATTTGA
1 TAATATTATATAATTTGA
47946 GTGATTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TAATATTATATAATTTGA
Found at i:53931 original size:21 final size:21
Alignment explanation
Indices: 53905--53963 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
53895 ATTATCCAAT
*
53905 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
53926 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
53947 CAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
53964 TAATAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:57845 original size:11 final size:12
Alignment explanation
Indices: 57815--57845 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57805 ACTAACGTAT
*
57815 GCATTTTTAGTG
1 GCATTTTTAGAG
57827 GCATTTTTAGAG
1 GCATTTTTAGAG
57839 GCATTTT
1 GCATTTT
57846 CACAAAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (12 bp):
GCATTTTTAGAG
Found at i:58350 original size:41 final size:41
Alignment explanation
Indices: 58305--58433 Score: 104
Period size: 41 Copynumber: 3.1 Consensus size: 41
58295 ACATGTGTAC
58305 AAAAATACCGCTAAAGTACTACTCTATTATGGCGTTTGTTG
1 AAAAATACCGCTAAAGTACTACTCTATTATGGCGTTTGTTG
* * * * *
58346 AAAAAAAGCCACTATAAATGA--AC-CTTATTGTGGCATTTGTAT-
1 AAAAATA-CCGCTA-AAGT-ACTACTC-TATTATGGCGTTTGT-TG
* * * *
58388 AAAAATGCCGCTAAAGTACTACTCTGTTACGGTGTTTGTTG
1 AAAAATACCGCTAAAGTACTACTCTATTATGGCGTTTGTTG
58429 AAAAA
1 AAAAA
58434 AATGCCATTA
Statistics
Matches: 65, Mismatches: 14, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
39 1 0.02
40 4 0.06
41 29 0.45
42 26 0.40
43 4 0.06
44 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
AAAAATACCGCTAAAGTACTACTCTATTATGGCGTTTGTTG
Found at i:58392 original size:83 final size:83
Alignment explanation
Indices: 58223--58740 Score: 411
Period size: 83 Copynumber: 6.3 Consensus size: 83
58213 TGTTTTTGGA
* * * * * * * * *
58223 AAAAAAACCACTAACGTACTACTCTTTTGCGGTGTTTGTTGAAAAACA-CCACTATAGATGAATC
1 AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAAAGCCACTATAGATGAACC
* * *
58287 CTATTACGACATGTGTAC
66 CTATTACGGCATTTGTAT
* * * * *
58305 AAAAATACCGCTAAAGTACTACTCTATTATGGCGTTTGTTGAAAAAAAGCCACTATAAATGAACC
1 AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAAAGCCACTATAGATGAACC
* **
58370 TTATTGTGGCATTTGTAT
66 CTATTACGGCATTTGTAT
** * * *
58388 AAAAATGCCGCTAAAGTACTACTCTGTTACGGTGTTTGTTGAAAAAAATGCCATTATAGATGAAC
1 AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAAA-GCCACTATAGATGAAC
** *
58453 CCTATTACAACATTTATAT
65 CCTATTACGGCATTTGTAT
* * * * * *
58472 AAAAACGCCGCTAAACTACTACTATGTTGCAGCGTTTGTTGAAAAAATGCCACTATAGATTAACC
1 AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAAAGCCACTATAGATGAACC
58537 CTATTACGG-AGTTTGTAT
66 CTATTACGGCA-TTTGTAT
* **** * * *
58555 AAAAACACCGCTAAAGTACTATTATGTTGTTACATTTATT-AAAAAAGGGCCACTATAGATGAAC
1 AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAA-AGCCACTATAGATGAAC
* * **
58619 CTTATTGCGGTGTTT-TAT
65 CCTATTACGGCATTTGTAT
* * * * * * * * * *
58637 ACAAACGCCACTAAAGAACTATTATGTTATGACGTTTGTTGAAAAAACGCCACTATGGAT-AAAC
1 AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAAAGCCACTATAGATGAACC
*
58701 CTATTGCGG--TGTTGTAT
66 CTATTACGGCAT-TTGTAT
** *
58718 AAAAACGTCGTTAAAGTACTACT
1 AAAAACACCGCTAAAGTACTACT
58741 TTGTCTCGGC
Statistics
Matches: 357, Mismatches: 71, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 31 0.09
82 93 0.26
83 162 0.45
84 68 0.19
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (83 bp):
AAAAACACCGCTAAAGTACTACTATGTTACGGCGTTTGTTGAAAAAAAGCCACTATAGATGAACC
CTATTACGGCATTTGTAT
Found at i:58512 original size:167 final size:165
Alignment explanation
Indices: 58223--58575 Score: 420
Period size: 167 Copynumber: 2.1 Consensus size: 165
58213 TGTTTTTGGA
* * * * * * *
58223 AAAAAAACCACTAACGTACTACTCTTTTGCGGTGTTTGTTGAAAAACACCACTATAGATGAATCC
1 AAAAACACCGCTAAAGTACTACTCTGTTACGGTGTTTGTTGAAAAAAACCACTATAGATGAACCC
* * * * * **
58288 TATTACGACATGTGTACAAAAATACCGCTAAAGTACTACTCTATTATGGCGTTTGTTGAAAAAAA
66 TATTACAACATGTATACAAAAACACCGCTAAACTACTACTATATTACAGCGTTTGTTGAAAAAAA
* **
58353 GCCACTATAAATGAACCTTATTGTGGCA-TTTGTAT
131 GCCACTATAAATGAACCCTATTACGG-AGTTTGTAT
** *
58388 AAAAATGCCGCTAAAGTACTACTCTGTTACGGTGTTTGTTGAAAAAAATGCCATTATAGATGAAC
1 AAAAACACCGCTAAAGTACTACTCTGTTACGGTGTTTGTTGAAAAAAA--CCACTATAGATGAAC
* * * * *
58453 CCTATTACAACATTTATATAAAAACGCCGCTAAACTACTACTATGTTGCAGCGTTTGTTGAAAAA
64 CCTATTACAACATGTATACAAAAACACCGCTAAACTACTACTATATTACAGCGTTTGTTGAAAAA
* * *
58518 ATGCCACTATAGATTAACCCTATTACGGAGTTTGTAT
129 AAGCCACTATAAATGAACCCTATTACGGAGTTTGTAT
58555 AAAAACACCGCTAAAGTACTA
1 AAAAACACCGCTAAAGTACTA
58576 TTATGTTGTT
Statistics
Matches: 156, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
165 41 0.26
166 1 0.01
167 114 0.73
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (165 bp):
AAAAACACCGCTAAAGTACTACTCTGTTACGGTGTTTGTTGAAAAAAACCACTATAGATGAACCC
TATTACAACATGTATACAAAAACACCGCTAAACTACTACTATATTACAGCGTTTGTTGAAAAAAA
GCCACTATAAATGAACCCTATTACGGAGTTTGTAT
Done.