Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009248.1 Hibiscus syriacus cultivar Beakdansim tig00112889_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: 120552
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4375 original size:25 final size:25
Alignment explanation
Indices: 4347--4405 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
4337 GTTGTGTGGT
*
4347 ATGTGATATGTCATCAG-TTTGGGTG
1 ATGTGATATGTCAT-AGTTTTAGGTG
*
4372 ATGTGATATGTCATTGTTTTAGGTG
1 ATGTGATATGTCATAGTTTTAGGTG
4397 ATGTGATAT
1 ATGTGATAT
4406 ACTTGAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.22, C:0.05, G:0.29, T:0.44
Consensus pattern (25 bp):
ATGTGATATGTCATAGTTTTAGGTG
Found at i:7395 original size:19 final size:19
Alignment explanation
Indices: 7359--7395 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
7349 TGAAAATGAT
*
7359 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
7378 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
7396 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:8819 original size:23 final size:23
Alignment explanation
Indices: 8774--8835 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
8764 CGGTAAAGCG
*
8774 CTACCGGTTTTGTTA-TTTTTTT
1 CTACCGATTTTGTTATTTTTTTT
8796 CTACCGATTTTGTTATTTTTTTT
1 CTACCGATTTTGTTATTTTTTTT
*
8819 CTATCGATTTTGTTATT
1 CTACCGATTTTGTTATT
8836 GTTAGGCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (23 bp):
CTACCGATTTTGTTATTTTTTTT
Found at i:9364 original size:20 final size:21
Alignment explanation
Indices: 9339--9378 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
9329 CTCTACATAG
9339 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
9359 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
9379 CCCAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:14253 original size:12 final size:12
Alignment explanation
Indices: 14236--14260 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14226 CGGAGACAAC
14236 ATTTTATATTAA
1 ATTTTATATTAA
14248 ATTTTATATTAA
1 ATTTTATATTAA
14260 A
1 A
14261 GGGTAAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTATATTAA
Found at i:16193 original size:29 final size:29
Alignment explanation
Indices: 16158--16222 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
16148 TAATTTATTC
16158 AATATTATGT-ATGCCAACATTATTATTAA
1 AATATTAT-TCATGCCAACATTATTATTAA
** *
16187 AATATTATTCATGTTAATATTATTATTAA
1 AATATTATTCATGCCAACATTATTATTAA
*
16216 ATTATTA
1 AATATTA
16223 AAATTAGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (29 bp):
AATATTATTCATGCCAACATTATTATTAA
Found at i:21106 original size:19 final size:19
Alignment explanation
Indices: 21084--21123 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21074 CAAAAAAAAC
*
21084 ATAATAT-AATATATATAAT
1 ATAATATCAATACATA-AAT
21103 ATAATATCAATACATAAAT
1 ATAATATCAATACATAAAT
21122 AT
1 AT
21124 CTTTAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATATCAATACATAAAT
Found at i:34551 original size:2 final size:2
Alignment explanation
Indices: 34544--34577 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34534 CTCTTCACAT
*
34544 TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
34578 ATGCTTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:39013 original size:39 final size:39
Alignment explanation
Indices: 38954--39043 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
38944 TATAATGAGG
38954 TGAATGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
1 TGAA-GATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
*
38994 TGAGGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
1 TGAAGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
39033 TGAAGATGGTG
1 TGAAGATGGTG
39044 AGAGTGAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 45 0.94
40 3 0.06
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (39 bp):
TGAAGATGGTGGTAATGAAGAAGCCTTTGACTTGCATCA
Found at i:49844 original size:24 final size:24
Alignment explanation
Indices: 49817--49932 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
49807 TTCGATTTGA
* *
49817 ATTCTAATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
49841 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
49865 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
49889 ATTCTGATCTGATACTTGATC-TAG
1 ATTCTGATATGATACTTGA-CATGG
*
49913 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
49933 CTGATTTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:49870 original size:12 final size:12
Alignment explanation
Indices: 49833--49895 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
49823 ATCTGATACT
49833 TGACATGGATTC
1 TGACATGGATTC
*
49845 TGATAT-GATATC
1 TGACATGGAT-TC
49857 TGACATGGATTC
1 TGACATGGATTC
* *
49869 TGATAT-GATAC
1 TGACATGGATTC
*
49880 TTGACTTGGATTC
1 -TGACATGGATTC
49893 TGA
1 TGA
49896 TCTGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:50116 original size:2 final size:2
Alignment explanation
Indices: 50109--50170 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
50099 ACGGATAGGG
50109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50151 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
50171 GTTTTAAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51875 original size:89 final size:89
Alignment explanation
Indices: 51724--51901 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
51714 GAGACAACGT
51724 GTAATTTACTCAAAAACGTAAAAACTATCATATCAAGACACATCGTCTTCTTCGTTAAACATTTA
1 GTAATTTACTCAAAAACGTAAAAACTATCATATCAAGACACATCGTCTTCTTCGTTAAACATTTA
51789 TCGACATATAATCGAAGTGAAAAA
66 TCGACATATAATCGAAGTGAAAAA
*
51813 GTAATTTACTCAAAATCGTAAAAACTATCATATCAAGACACATCGTCTTCTTCGTTAAACATTTA
1 GTAATTTACTCAAAAACGTAAAAACTATCATATCAAGACACATCGTCTTCTTCGTTAAACATTTA
*
51878 TCGACATATAATTGAAGTGAAAAA
66 TCGACATATAATCGAAGTGAAAAA
51902 ATATAACGTT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (89 bp):
GTAATTTACTCAAAAACGTAAAAACTATCATATCAAGACACATCGTCTTCTTCGTTAAACATTTA
TCGACATATAATCGAAGTGAAAAA
Found at i:69019 original size:21 final size:20
Alignment explanation
Indices: 68994--69036 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
68984 TTTAACATAA
68994 CAAAGGAAATATTGATACTTC
1 CAAAGGAAATATTGATA-TTC
* *
69015 CAAAGGCAGTATTGATATTC
1 CAAAGGAAATATTGATATTC
69035 CA
1 CA
69037 TATATAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (20 bp):
CAAAGGAAATATTGATATTC
Found at i:70341 original size:2 final size:2
Alignment explanation
Indices: 70336--70368 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
70326 ATATTTTTTC
70336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70369 GTTGAGATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78956 original size:9 final size:10
Alignment explanation
Indices: 78932--78974 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
78922 TCATTTTTGT
78932 TAAAAATAAA
1 TAAAAATAAA
*
78942 TAAAAATGAA
1 TAAAAATAAA
* *
78952 TAAAATTCAA
1 TAAAAATAAA
78962 TAAAAATATAA
1 TAAAAATA-AA
78973 TA
1 TA
78975 TAAAGCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:79516 original size:10 final size:10
Alignment explanation
Indices: 79491--79538 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
79481 TTTACAATAT
*
79491 ATTTTTATTG
1 ATTTTTATTC
* *
79501 AATTTTGTTC
1 ATTTTTATTC
79511 ATTTTTAATTC
1 ATTTTT-ATTC
*
79522 ATTTTTATTT
1 ATTTTTATTC
79532 ATTTTTA
1 ATTTTTA
79539 AAAAAATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:90361 original size:4 final size:4
Alignment explanation
Indices: 90352--90410 Score: 118
Period size: 4 Copynumber: 14.8 Consensus size: 4
90342 ACAATACATG
90352 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
90400 ATAC ATAC ATA
1 ATAC ATAC ATA
90411 TGGTGCAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:94364 original size:2 final size:2
Alignment explanation
Indices: 94353--94480 Score: 92
Period size: 2 Copynumber: 66.5 Consensus size: 2
94343 AATATAAGTG
*
94353 TA TA -A TA TA TA TA -A GTA TA TA T- TA TA TA TA -A GTG 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
* * * *
94393 TA -A T- TA TA TA AA TA TA TA TA TG TA TA TA CT- TA TG TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
** * *
94433 TA TA T- TA TA CG TG TG 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
94474 TA TA TA T
1 TA TA TA T
94481 GTTACACATA
Statistics
Matches: 103, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
1 8 0.08
2 93 0.90
3 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:94366 original size:17 final size:17
Alignment explanation
Indices: 94344--94394 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
94334 TATATTTATA
94344 ATATAAGTGTATAATAT
1 ATATAAGTGTATAATAT
* *
94361 ATATAAGTATATATTAT
1 ATATAAGTGTATAATAT
94378 ATATAAGTGTAT-ATAT
1 ATATAAGTGTATAATAT
94394 A
1 A
94395 ATTATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (17 bp):
ATATAAGTGTATAATAT
Found at i:94598 original size:7 final size:8
Alignment explanation
Indices: 94584--94645 Score: 80
Period size: 7 Copynumber: 8.4 Consensus size: 8
94574 ATGCATATGC
94584 ATAAGTAT
1 ATAAGTAT
94592 A-AAGTAT
1 ATAAGTAT
94599 ATAA-TAT
1 ATAAGTAT
94606 ATAAGTAT
1 ATAAGTAT
94614 A-AAGTAT
1 ATAAGTAT
94621 ATAA-TAT
1 ATAAGTAT
94628 ATAAGTAT
1 ATAAGTAT
*
94636 A-AAATAT
1 ATAAGTAT
94643 ATA
1 ATA
94646 CATAAGCAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
7 34 0.71
8 14 0.29
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (8 bp):
ATAAGTAT
Found at i:94611 original size:15 final size:16
Alignment explanation
Indices: 94584--94645 Score: 80
Period size: 15 Copynumber: 4.2 Consensus size: 16
94574 ATGCATATGC
94584 ATAAGTATA-AAGTAT
1 ATAAGTATATAAGTAT
94599 ATAA-TATATAAGTAT
1 ATAAGTATATAAGTAT
94614 A-AAGTATATAA-TAT
1 ATAAGTATATAAGTAT
*
94628 ATAAGTATA-AAATAT
1 ATAAGTATATAAGTAT
94643 ATA
1 ATA
94646 CATAAGCAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (16 bp):
ATAAGTATATAAGTAT
Found at i:94612 original size:22 final size:22
Alignment explanation
Indices: 94584--94645 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
94574 ATGCATATGC
94584 ATAAGTATAAAGTATATAATAT
1 ATAAGTATAAAGTATATAATAT
94606 ATAAGTATAAAGTATATAATAT
1 ATAAGTATAAAGTATATAATAT
*
94628 ATAAGTATAAAATATATA
1 ATAAGTATAAAGTATATA
94646 CATAAGCAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAAGTATAAAGTATATAATAT
Found at i:94709 original size:12 final size:12
Alignment explanation
Indices: 94694--94823 Score: 79
Period size: 12 Copynumber: 11.0 Consensus size: 12
94684 ATGTACACAA
94694 GTATATATATAT
1 GTATATATATAT
* *
94706 GTATGTATGTAT
1 GTATATATATAT
* *
94718 ATATAGATA-AT
1 GTATATATATAT
94729 -TATATATA-A-
1 GTATATATATAT
* *
94738 GTATATACATAA
1 GTATATATATAT
*
94750 GTATATATATAA
1 GTATATATATAT
* *
94762 GTACATATATAA
1 GTATATATATAT
*
94774 GTATATACATAGGT
1 GTATATATATA--T
* * *
94788 GTGTGTGTATAT
1 GTATATATATAT
*
94800 ATATATATATAT
1 GTATATATATAT
*
94812 ATATATATATAT
1 GTATATATATAT
94824 ATAGCATTAT
Statistics
Matches: 92, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
10 15 0.16
11 3 0.03
12 67 0.73
14 7 0.08
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (12 bp):
GTATATATATAT
Found at i:94824 original size:12 final size:11
Alignment explanation
Indices: 94716--94844 Score: 70
Period size: 12 Copynumber: 11.6 Consensus size: 11
94706 GTATGTATGT
*
94716 ATATATAGATA
1 ATATATATATA
94727 AT-TATATATA
1 ATATATATATA
*
94737 AGTATATACATA
1 A-TATATATATA
94749 AGTATATATATA
1 A-TATATATATA
*
94761 AGTACATATATA
1 A-TATATATATA
*
94773 AGTATATACATA
1 A-TATATATATA
* * * * *
94785 GGTGTGTGTGT-
1 -ATATATATATA
94796 ATATATATAT-
1 ATATATATATA
94806 ATATATATAT-
1 ATATATATATA
94816 ATATATATATA
1 ATATATATATA
**
94827 GCAT-TATATA
1 ATATATATATA
94837 AGTATATA
1 A-TATATA
94845 ATTAAACATG
Statistics
Matches: 91, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
10 39 0.43
11 7 0.08
12 45 0.49
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (11 bp):
ATATATATATA
Found at i:94844 original size:2 final size:2
Alignment explanation
Indices: 94695--94826 Score: 69
Period size: 2 Copynumber: 67.0 Consensus size: 2
94685 TGTACACAAG
* * * *
94695 TA TA TA TA TA TG TA TG TA TG TA TA TA TA GA TA -A T- 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
* *
94735 TA -A GTA TA TA CA TA -A GTA TA TA TA TA -A GTA CA TA TA TA -A
1 TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
* ** * * * *
94774 GTA TA TA CA TA GG TG TG TG 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
94817 TA TA TA TA TA
1 TA TA TA TA TA
94827 GCATTATATA
Statistics
Matches: 102, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
1 6 0.06
2 92 0.90
3 4 0.04
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (2 bp):
TA
Found at i:96487 original size:4 final size:4
Alignment explanation
Indices: 96478--96588 Score: 57
Period size: 4 Copynumber: 26.5 Consensus size: 4
96468 GATCCCTTCG
* ** *
96478 AATA AATA AATTC AA-A AATA AAT- AATA AATA AATA TTTTGA AATA AATT
1 AATA AATA AA-TA AATA AATA AATA AATA AATA AATA -AAT-A AATA AATA
* * * *
96527 ATTA TAA-A AATA AATA AATT ATTCAA AATA AATA AATA ATTCA AAGTA
1 AATA -AATA AATA AATA AATA AAT--A AATA AATA AATA AAT-A AA-TA
96575 AATA AATA AATA AA
1 AATA AATA AATA AA
96589 AATTACCTCC
Statistics
Matches: 80, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
3 7 0.09
4 58 0.73
5 11 0.14
6 4 0.05
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (4 bp):
AATA
Found at i:96556 original size:18 final size:18
Alignment explanation
Indices: 96518--96581 Score: 83
Period size: 18 Copynumber: 3.4 Consensus size: 18
96508 AAATATTTTG
*
96518 AAATAAATTATTATAAAAAT
1 AAATAAATTA-T-TCAAAAT
96538 AAATAAATTATTCAAAAT
1 AAATAAATTATTCAAAAT
* *
96556 AAATAAATAATTCAAAGT
1 AAATAAATTATTCAAAAT
96574 AAATAAAT
1 AAATAAAT
96582 AAATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
18 30 0.73
19 1 0.02
20 10 0.24
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATAAATTATTCAAAAT
Found at i:96582 original size:18 final size:18
Alignment explanation
Indices: 96533--96583 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
96523 AATTATTATA
*
96533 AAAATAAATAAATTATTC
1 AAAATAAATAAATAATTC
96551 AAAATAAATAAATAATTC
1 AAAATAAATAAATAATTC
*
96569 AAAGTAAATAAATAA
1 AAAATAAATAAATAA
96584 ATAAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATAAATAAATAATTC
Found at i:100625 original size:42 final size:42
Alignment explanation
Indices: 100539--100646 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
100529 ACCCGAAGGT
* * * *
100539 CTTATAGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
*
100580 CTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
100622 CTTACT-GATGACCCGAAGGATTTAA
1 CTTA-TAGATGACCCGAAGGATTTAA
100647 AAATCAAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 20 0.34
42 38 0.64
43 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
Found at i:100803 original size:88 final size:88
Alignment explanation
Indices: 100628--100996 Score: 480
Period size: 88 Copynumber: 4.2 Consensus size: 88
100618 AAGACTTACT
* * *
100628 GATGACCCGAAGGATTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTT-TTAAAATATCATTTGA
1 GATGACCCGAAGGACTTACAAATC-AGAAACCCC-GAAGGCTTAGTTTCTT-AAATCTCATTTGA
*
100692 AAACATTTTGCACTGAAGGTCTTATG
63 AAACATCTTGCACTGAAGGTCTTATG
* *
100718 GATGACCGGAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTTAATAT-TTA-TTGAA
1 GATGACCCGAAGGACTTACAAATC-AGAAACCCCGAAGGCTTAGTTTCTTAA-ATCTCATTTGAA
* *
100781 AACATCATGTACTGAAGGTCTTATG
64 AACATCTTGCACTGAAGGTCTTATG
* **
100806 GATGACCCGAAGGACTTATAAATCCTAAACCCCGAAGGCTTAGTTTC-TAAATCTCATTTG-AAA
1 GATGACCCGAAGGACTTACAAATCAGAAACCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAA
*
100869 CATCTTGCACTGAAGGTTTTATG
66 CATCTTGCACTGAAGGTCTTATG
*
100892 GATGGCCCGAAGGACTTACAAATCAGAAACCCTCGAAGGCTTAGTTTCTTAAATCTCATTTGAAA
1 GATGACCCGAAGGACTTACAAATCAGAAACCC-CGAAGGCTTAGTTTCTTAAATCTCATTTGAAA
* *
100957 ACATCCTGCACT-ATAGGTCTTATT
65 ACATCTTGCACTGA-AGGTCTTATG
* *
100981 GATGGCCCGAAAGACT
1 GATGACCCGAAGGACT
100997 CATCTTACTC
Statistics
Matches: 248, Mismatches: 23, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
85 2 0.01
86 56 0.23
87 39 0.16
88 63 0.25
89 53 0.21
90 35 0.14
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (88 bp):
GATGACCCGAAGGACTTACAAATCAGAAACCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAAA
CATCTTGCACTGAAGGTCTTATG
Found at i:100893 original size:174 final size:179
Alignment explanation
Indices: 100628--100996 Score: 511
Period size: 174 Copynumber: 2.1 Consensus size: 179
100618 AAGACTTACT
* *
100628 GATGACCCGAAGGATTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTTTTAAAATATCATTTGAA
1 GATGACCCGAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATATCATTTGAA
* *
100693 AACATTTTGCACTGAAGGTCTTATGGATGACCGGAAGGACTTACAAATCAAGAAACCC-CGAAGG
66 AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATC-AGAAACCCTCGAAGG
* *
100757 CTTAGTTTCTTAATAT-TTA-TTGAAAACATCATGTACTGA-AGGTCTTATG
130 CTTAGTTTCTTAA-ATCTCATTTGAAAACATCATGCACT-ATAGGTCTTATG
* ** *
100806 GATGACCCGAAGGACTTATAAATC-CTAAACCCC-GAAGGCTTAGTTTCT-AAATCTCATTTG-A
1 GATGACCCGAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATATCATTTGAA
* *
100867 AACATCTTGCACTGAAGGTTTTATGGATGGCCCGAAGGACTTACAAATCAGAAACCCTCGAAGGC
66 AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAGAAACCCTCGAAGGC
* *
100932 TTAGTTTCTTAAATCTCATTTGAAAACATCCTGCACTATAGGTCTTATT
131 TTAGTTTCTTAAATCTCATTTGAAAACATCATGCACTATAGGTCTTATG
* *
100981 GATGGCCCGAAAGACT
1 GATGACCCGAAGGACT
100997 CATCTTACTC
Statistics
Matches: 171, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
173 10 0.06
174 68 0.40
175 50 0.29
176 14 0.08
177 7 0.04
178 22 0.13
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (179 bp):
GATGACCCGAAGGACTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTTCTAAAATATCATTTGAA
AACATCTTGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAGAAACCCTCGAAGGC
TTAGTTTCTTAAATCTCATTTGAAAACATCATGCACTATAGGTCTTATG
Found at i:101051 original size:42 final size:42
Alignment explanation
Indices: 101004--101102 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
100994 ACTCATCTTA
* * **
101004 CTCGAAAGACTTA-TAGATGAGCTGAAGGATTTACGCATCATG
1 CTCGAAAGACTTACT-GATGACCCGAAGGATTTAAACATCATG
101046 CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
1 CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
101088 CTCG-AAGACTTACTG
1 CTCGAAAGACTTACTG
101103 TTGGCCCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 11 0.21
42 40 0.77
43 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
Found at i:101126 original size:41 final size:42
Alignment explanation
Indices: 101004--101126 Score: 133
Period size: 42 Copynumber: 3.0 Consensus size: 42
100994 ACTCATCTTA
* ** *
101004 CTCGAAAGACTTA-TAGATGAGCTGAAGGATTTACGCATCATG
1 CTCGAAAGACTTACT-GATGACCCAAAGGATTTACACATCATG
* *
101046 CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
1 CTCGAAAGACTTACTGATGACCCAAAGGATTTACACATCATG
* * * *
101088 CTCG-AAGACTTACTGTTGGCCCAAAGGACTTACTCATCA
1 CTCGAAAGACTTACTGATGACCCAAAGGATTTACACATCA
101127 AGAAACCCCC
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 29 0.41
42 40 0.57
43 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCAAAGGATTTACACATCATG
Found at i:101272 original size:42 final size:42
Alignment explanation
Indices: 101168--101459 Score: 442
Period size: 42 Copynumber: 7.0 Consensus size: 42
101158 TCACCAAACA
* * **
101168 AACCCTACATATCACGTTGGTCCCTCAAG-TTATCATTTAGG
1 AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
* *
101209 AACCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAG
1 AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
*
101251 AACCCTACATATCACGATGGTCCCTCAAGCTTGTTATCAAGG
1 AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
*
101293 AACCCTACATATCACGTTTGGTCCCTCAAGCTTGTCATCAAGG
1 AACCCTACATATCACG-ATGGTCCCTCAAGCTTGTCATCAAGG
* * *
101336 AACCCTACATATCACGATAGTCCTTCAAGCTTGTCATTAAGG
1 AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
* *
101378 AACCCTATATATCACGATGTTCCCTCAAGCTTGTCATCAAGG
1 AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
*
101420 AACCCTACATATTACGATGGTCCCTCAAGCTTGTCATCAA
1 AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAA
101460 TGCGAACCTT
Statistics
Matches: 228, Mismatches: 21, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
41 29 0.13
42 159 0.70
43 40 0.18
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (42 bp):
AACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
Found at i:101350 original size:127 final size:126
Alignment explanation
Indices: 101168--101459 Score: 451
Period size: 127 Copynumber: 2.3 Consensus size: 126
101158 TCACCAAACA
* ** * *
101168 AACCCTACATATCACGTTGGTCCCTCAAG-TTATCATTTAGGAACCCTACATATCACGTTGGTCC
1 AACCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAGGAACCCTACATATCACGATAGTCC
*
101232 CTCAAGCTTGTCATCAAAGAACCCTACATATCACGATGGTCCCTCAAGCTTGTTATCAAGG
66 CTCAAGCTTGTCATCAAAGAACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
101293 AACCCTACATATCACGTTTGGTCCCTCAAGCTTGTCATCAAGGAACCCTACATATCACGATAGTC
1 AACCCTACATATCACG-TTGGTCCCTCAAGCTTGTCATCAAGGAACCCTACATATCACGATAGTC
* * * * *
101358 CTTCAAGCTTGTCATTAAGGAACCCTATATATCACGATGTTCCCTCAAGCTTGTCATCAAGG
65 CCTCAAGCTTGTCATCAAAGAACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
* *
101420 AACCCTACATATTACGATGGTCCCTCAAGCTTGTCATCAA
1 AACCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAA
101460 TGCGAACCTT
Statistics
Matches: 152, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 16 0.11
126 36 0.24
127 100 0.66
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (126 bp):
AACCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAGGAACCCTACATATCACGATAGTCC
CTCAAGCTTGTCATCAAAGAACCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
Found at i:101644 original size:105 final size:105
Alignment explanation
Indices: 101462--101748 Score: 510
Period size: 105 Copynumber: 2.8 Consensus size: 105
101452 GTCATCAATG
*
101462 CGAACCTTCTCCTTTAGGACGATTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTC
1 CGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTC
*
101527 CTTCTGCGGTGGATTTGAAAGGAACATGCTATTCTCATTA
66 CTTCTGCGGTGGATTTGAAAGGAACAAGCTATTCTCATTA
101567 CGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTC
1 CGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTC
*
101632 CTTCTGCGGTGGATTTGAAAGGAACAAGCTCTTCTCATTA
66 CTTCTGCGGTGGATTTGAAAGGAACAAGCTATTCTCATTA
*
101672 CGAACCTTCTCC-TTAGGACGAGTTCTTCTGATTATGAACTCTTCTGGAAATGTTGG-TCACCTC
1 CGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTC
101735 CTTCT--GGTGGATTT
66 CTTCTGCGGTGGATTT
101749 ATTGTTGTTG
Statistics
Matches: 178, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
101 9 0.05
103 12 0.07
104 43 0.24
105 114 0.64
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (105 bp):
CGAACCTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTC
CTTCTGCGGTGGATTTGAAAGGAACAAGCTATTCTCATTA
Found at i:102682 original size:8 final size:8
Alignment explanation
Indices: 102671--102780 Score: 84
Period size: 8 Copynumber: 14.0 Consensus size: 8
102661 TTCTTTTTTC
102671 TTTTCATT
1 TTTTCATT
102679 TTTTCATT
1 TTTTCATT
**
102687 TTTTTTTT
1 TTTTCATT
**
102695 TTTTTTTT
1 TTTTCATT
102703 TTTTC-TT
1 TTTTCATT
*
102710 TTTT-TTT
1 TTTTCATT
**
102717 TTTTTTTT
1 TTTTCATT
**
102725 TTTTTTTT
1 TTTTCATT
102733 TTTTCATTTT
1 TTTTCA--TT
102743 TTTTCATT
1 TTTTCATT
102751 TTTTC--T
1 TTTTCATT
*
102757 TTTTCACT
1 TTTTCATT
102765 TTTTCATT
1 TTTTCATT
102773 TTTTCATT
1 TTTTCATT
102781 CATTCTTTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.07
7 12 0.13
8 64 0.71
10 8 0.09
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTCATT
Found at i:102694 original size:32 final size:31
Alignment explanation
Indices: 102658--102776 Score: 125
Period size: 30 Copynumber: 3.8 Consensus size: 31
102648 CGAACCCTCC
102658 TTTTTCTTTTTTCTTTTCATTTTTTCATTTTT
1 TTTTTCTTTTTTCTTTTCATTTTTT-ATTTTT
* * *
102690 TTTTTTTTTTTTTTTTTC-TTTTTTTTTTTT
1 TTTTTCTTTTTTCTTTTCATTTTTTATTTTT
* * **
102720 TTTTTTTTTTTTTTTTTCATTTTTT-TTCAT
1 TTTTTCTTTTTTCTTTTCATTTTTTATTTTT
*
102750 TTTTTCTTTTTCACTTTTTCATTTTTT
1 TTTTTCTTTTT-TC-TTTTCATTTTTT
102777 CATTCATTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
30 36 0.47
31 12 0.16
32 28 0.37
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (31 bp):
TTTTTCTTTTTTCTTTTCATTTTTTATTTTT
Found at i:102716 original size:54 final size:54
Alignment explanation
Indices: 102658--102761 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
102648 CGAACCCTCC
** *
102658 TTTTTCTTTTTTCTTTTCATTTTTTCATTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTTCATTTTTTCATTTTTTTTCATTTTTTCTTTTTCTTTT
* * **
102712 TTTTTTTTTTTTTTTTTTTTTTTTTCATTTTTTTTCATTTTTTCTTTTTC
1 TTTTTCTTTTTTCTTTTCATTTTTTCATTTTTTTTCATTTTTTCTTTTTC
102762 ACTTTTTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.88
Consensus pattern (54 bp):
TTTTTCTTTTTTCTTTTCATTTTTTCATTTTTTTTCATTTTTTCTTTTTCTTTT
Found at i:102776 original size:1 final size:1
Alignment explanation
Indices: 102685--102760 Score: 98
Period size: 1 Copynumber: 76.0 Consensus size: 1
102675 CATTTTTTCA
* ** **
102685 TTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCATTTTTTTTCAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
102750 TTTTTCTTTTT
1 TTTTTTTTTTT
102761 CACTTTTTCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.03, C:0.05, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:102780 original size:30 final size:29
Alignment explanation
Indices: 102659--102777 Score: 106
Period size: 32 Copynumber: 4.2 Consensus size: 29
102649 GAACCCTCCT
102659 TTTTCTTTTTTC-TTTTCATTTTTTCA-T
1 TTTTCTTTTTTCTTTTTCATTTTTTCATT
*
102686 TTTT-TTTTTT-TTTTT--TTTTTTCTTTT
1 TTTTCTTTTTTCTTTTTCATTTTTTC-ATT
* * **
102712 TTTTTTTTTTTTTTTTTTTTTTTTTCATTTT
1 TTTTCTTTTTTCTTTTTCATTTTTTCA--TT
*
102743 TTTTCATTTTTTCTTTTTCACTTTTTCATT
1 TTTTC-TTTTTTCTTTTTCATTTTTTCATT
102773 TTTTC
1 TTTTC
102778 ATTCATTCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.09
26 15 0.20
27 10 0.13
28 5 0.07
30 14 0.19
31 6 0.08
32 18 0.24
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (29 bp):
TTTTCTTTTTTCTTTTTCATTTTTTCATT
Found at i:102787 original size:30 final size:31
Alignment explanation
Indices: 102732--102790 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
102722 TTTTTTTTTT
**
102732 TTTTTCATTTTTTTTCATTTTTTCTTTTTCAC
1 TTTTTCA-TTTTTTTCATTCATTCTTTTTCAC
102764 TTTTTCA-TTTTTTCATTCATTCTTTTT
1 TTTTTCATTTTTTTCATTCATTCTTTTT
102791 TTTTCAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
32 7 0.28
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTTCATTTTTTTCATTCATTCTTTTTCAC
Found at i:102788 original size:22 final size:21
Alignment explanation
Indices: 102728--102790 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
102718 TTTTTTTTTT
* *
102728 TTTTTTTTTCATTTTTTTTCA
1 TTTTTTCTTCATTCTTTTTCA
*
102749 TTTTTTCTT-TTTCACTTTTTCA
1 TTTTTTCTTCATT--CTTTTTCA
102771 TTTTTTCATTCATTCTTTTT
1 TTTTTTC-TTCATTCTTTTT
102791 TTTTCAAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 2 0.06
21 8 0.24
22 20 0.59
23 2 0.06
24 2 0.06
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTCTTCATTCTTTTTCA
Found at i:106334 original size:14 final size:14
Alignment explanation
Indices: 106315--106341 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
106305 AAATGAATGT
106315 AAAGAATGAAGAAC
1 AAAGAATGAAGAAC
106329 AAAGAATGAAGAA
1 AAAGAATGAAGAA
106342 TGAAAATGTA
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:0.67, C:0.04, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAGAATGAAGAAC
Found at i:118319 original size:41 final size:42
Alignment explanation
Indices: 118262--118369 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
118252 ACCCGAAGGT
* *
118262 CTTATAGATGGCCCGAAGGACTT-ATCATCT-TGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCAT-TATGCTCGAAAGA
*
118303 CTTATAGATGACCCGAAGGATTTAAGCATTATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGACTTAAGCATTATGCTCGAAAGA
*
118345 CTTACT-GATGACCCGAAGGATTTAA
1 CTTA-TAGATGACCCGAAGGACTTAA
118370 AAATCAAGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
41 22 0.36
42 38 0.62
43 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGACTTAAGCATTATGCTCGAAAGA
Found at i:118509 original size:90 final size:90
Alignment explanation
Indices: 118351--118728 Score: 535
Period size: 90 Copynumber: 4.2 Consensus size: 90
118341 AAGACTTACT
* * * *
118351 GATGACCCGAAGGATTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTT-TTAAAATCTCATTTGG
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTT-AAATCTCATTTGA
118415 AAACATCCTGCACTGAAGGTCTTATG
65 AAACATCCTGCACTGAAGGTCTTATG
* *
118441 GATAACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTTATTTGAA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
** * *
118506 AACATTATGTACTAAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* * * *
118531 GATGGCCCGAAGGACTTATAAATCAAGAAACCCCCAAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
*
118596 AACATCCTGCACTGAAAGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* *
118621 GATGGCCTGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
* *
118686 AACATCCTGCACT-ATAGGTATTATA
66 AACATCCTGCACTGA-AGGTCTTATG
* *
118711 GATGGCCTGAAGGACTTA
1 GATGACCCGAAGGACTTA
118729 TCATCTTGCT
Statistics
Matches: 258, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
89 1 0.00
90 255 0.99
91 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (90 bp):
GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
AACATCCTGCACTGAAGGTCTTATG
Found at i:118792 original size:22 final size:21
Alignment explanation
Indices: 118767--118834 Score: 50
Period size: 22 Copynumber: 3.2 Consensus size: 21
118757 GTTAAAGGAT
118767 TTACGCATCATGCTCGAAAGAC
1 TTAC-CATCATGCTCGAAAGAC
* * * *
118789 TTA-C-TGATGACCCGAAGGAT
1 TTACCATCATG-CTCGAAAGAC
*
118809 TTAAACATCATGCTCGAAAGAC
1 TT-ACCATCATGCTCGAAAGAC
118831 TTAC
1 TTAC
118835 TGTTGGCCCA
Statistics
Matches: 33, Mismatches: 9, Indels: 9
0.65 0.18 0.18
Matches are distributed among these distances:
19 4 0.12
20 10 0.30
21 2 0.06
22 13 0.39
23 4 0.12
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (21 bp):
TTACCATCATGCTCGAAAGAC
Found at i:118860 original size:42 final size:42
Alignment explanation
Indices: 118711--118860 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 42
118701 AGGTATTATA
** *
118711 GATGGCCTGAAGGACTTA-TCATCTTGCTCGAAAGACTTA-T
1 GATGGCCCAAAGGACTTACTCATCATGCTCGAAAGACTTACT
** * *
118751 AGATGAG-TTAAAGGATTTACGCATCATGCTCGAAAGACTTACT
1 -GATG-GCCCAAAGGACTTACTCATCATGCTCGAAAGACTTACT
* * * **
118794 GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACT
1 GATGGCCCAAAGGACTTACTCATCATGCTCGAAAGACTTACT
*
118836 GTTGGCCCAAAGGACTTACTCATCA
1 GATGGCCCAAAGGACTTACTCATCA
118861 AGAAACCCCT
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
41 13 0.15
42 74 0.84
43 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
GATGGCCCAAAGGACTTACTCATCATGCTCGAAAGACTTACT
Found at i:118978 original size:22 final size:22
Alignment explanation
Indices: 118953--119017 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
118943 AACCCCTACA
118953 TATCACGTTGGTCCCTCAAGCT
1 TATCACGTTGGTCCCTCAAGCT
** * * *
118975 TATCATC-AAGGACCC-CTA-CA
1 TATCA-CGTTGGTCCCTCAAGCT
118995 TATCACGTTGGTCCCTCAAGCT
1 TATCACGTTGGTCCCTCAAGCT
119017 T
1 T
119018 GTCATCAAAG
Statistics
Matches: 29, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 4 0.14
22 12 0.41
23 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.29
Consensus pattern (22 bp):
TATCACGTTGGTCCCTCAAGCT
Found at i:119042 original size:85 final size:86
Alignment explanation
Indices: 118889--119274 Score: 573
Period size: 85 Copynumber: 4.5 Consensus size: 86
118879 AGTTTCTTAG
* *
118889 TTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG--TGTTCATCAAGGAACCCCTAC
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTG-TCATCAAAGAACCCCTAC
*
118952 ATATCACGTTGGTCCCTCAAGC
65 ATATCACGATGGTCCCTCAAGC
*
118974 TTATCATCAAGG-ACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAGAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAGAACCCCTACA
*
119038 TATCACAATGGTCCCTCAAGC
66 TATCACGATGGTCCCTCAAGC
* * * *
119059 TTGTTATCAAGGAACCCCTACATATCACTTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAGAACCCCTACA
*
119124 TATCACGATGGTCCCTTAAGC
66 TATCACGATGGTCCCTCAAGC
* * * * * *
119145 TTGTCATTAAGGAACCCTTACCTATCACGATGTTCCCTCAAGCTTGTCATC-AAGGACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAGAACCCCTACA
119209 TATCACGATGGTCCCTCAAGC
66 TATCACGATGGTCCCTCAAGC
* *
119230 TTGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAGCTT
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTT
119275 AGTTTCTTAT
Statistics
Matches: 270, Mismatches: 28, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
84 29 0.11
85 128 0.47
86 113 0.42
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (86 bp):
TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAGAACCCCTACA
TATCACGATGGTCCCTCAAGC
Found at i:119050 original size:43 final size:43
Alignment explanation
Indices: 118889--119274 Score: 582
Period size: 43 Copynumber: 9.0 Consensus size: 43
118879 AGTTTCTTAG
* *
118889 TTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG-
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
*
118931 -TGTTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
1 TTG-TCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* *
118974 TTATCATCAAGG-ACCCCTACATATCACGTTGGTCCCTCAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* *
119016 TTGTCATCAAAGAACCCCTACATATCACAATGGTCCCTCAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* **
119059 TTGTTATCAAGGAACCCCTACATATCACTTTGGTCCCTCAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* *
119102 TTATCATCAAGGAACCCCTACATATCACGATGGTCCCTTAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* * * *
119145 TTGTCATTAAGGAACCCTTACCTATCACGATGTTCCCTCAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
119188 TTGTCATCAAGG-ACCCCTACATATCACGATGGTCCCTCAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
*
119230 TTGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
119273 TT
1 TT
119275 AGTTTCTTAT
Statistics
Matches: 313, Mismatches: 26, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.01
42 117 0.37
43 193 0.62
44 1 0.00
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (43 bp):
TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
Found at i:119139 original size:171 final size:171
Alignment explanation
Indices: 118889--119275 Score: 593
Period size: 171 Copynumber: 2.3 Consensus size: 171
118879 AGTTTCTTAG
* *
118889 TTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG-TGT-TCATCAAGGAACCCCTAC
1 TTGTCATCAAGGAACCCCTACATATCACTTTGGTCCCTCAAGCT-TATCATCAAGGAACCCCTAC
* *
118952 ATATCACGTTGGTCCCTCAAGCTTATCATCAAGG-ACCCCTACATATCACGTTGGTCCCTCAAGC
65 ATATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
119016 TTGTCATCAAAGAACCCCTACATATCACAATGGTCCCTCAAGC
130 TTGTCATC-AAGAACCCCTACATATCACAATGGTCCCTCAAGC
*
119059 TTGTTATCAAGGAACCCCTACATATCACTTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACTTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACA
* * * * * *
119124 TATCACGATGGTCCCTTAAGCTTGTCATTAAGGAACCCTTACCTATCACGATGTTCCCTCAAGCT
66 TATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCT
* *
119189 TGTCATCAAGGACCCCTACATATCACGATGGTCCCTCAAGC
131 TGTCATCAAGAACCCCTACATATCACAATGGTCCCTCAAGC
*
119230 TTGTCATCAAGGAACCCCTACATATCA-TGATGGTCCCTCAAGCTTA
1 TTGTCATCAAGGAACCCCTACATATCACT-TTGGTCCCTCAAGCTTA
119276 GTTTCTTATA
Statistics
Matches: 198, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
170 41 0.21
171 123 0.62
172 34 0.17
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (171 bp):
TTGTCATCAAGGAACCCCTACATATCACTTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACA
TATCACGATGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCT
TGTCATCAAGAACCCCTACATATCACAATGGTCCCTCAAGC
Found at i:119204 original size:128 final size:129
Alignment explanation
Indices: 118889--119274 Score: 600
Period size: 128 Copynumber: 3.0 Consensus size: 129
118879 AGTTTCTTAG
* *
118889 TTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG--TGTTCATCAAGGAACCCCTAC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTG-TCATCAAGGAACCCCTAC
*
118952 ATATCACGTTGGTCCCTCAAGCTTATCATCAAGG-ACCCCTACATATCACGTTGGTCCCTCAAGC
65 ATATCACGTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* * *
119016 TTGTCATCAAAGAACCCCTACATATCACAATGGTCCCTCAAGCTTGTTATCAAGGAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACA
* *
119081 TATCACTTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTTAAGC
66 TATCACGTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
* * * *
119145 TTGTCATTAAGGAACCCTTACCTATCACGATGTTCCCTCAAGCTTGTCATCAAGG-ACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACA
* * *
119209 TATCACGATGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAGC
66 TATCACGTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
119273 TT
1 TT
119275 AGTTTCTTAT
Statistics
Matches: 236, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
127 38 0.16
128 120 0.51
129 78 0.33
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (129 bp):
TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGGAACCCCTACA
TATCACGTTGGTCCCTCAAGCTTATCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGC
Done.