Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001110.1 Hibiscus syriacus cultivar Beakdansim tig00002192_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: 85532
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:866 original size:12 final size:12
Alignment explanation
Indices: 851--910 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
841 TAGAAATCAA
851 AACAGAATTCAG
1 AACAGAATTCAG
*
863 AACA-TATATCAG
1 AACAGAAT-TCAG
* *
875 AACAGAATCCAT
1 AACAGAATTCAG
* *
887 ATCAGAAATCAG
1 AACAGAATTCAG
899 AACAGAATTCAG
1 AACAGAATTCAG
911 GTCATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:878 original size:24 final size:24
Alignment explanation
Indices: 846--933 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
836 GATATTAGAA
* *
846 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGATCATAT
* * * *
870 ATCAGAACAGAATCCATATCAGAA
1 ATCAGAACAGAATTCAGATCATAT
* *
894 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGATCATAT
*
918 ATCAGAAAAGAATTCA
1 ATCAGAACAGAATTCA
934 AGTCGAAAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCATAT
Found at i:945 original size:24 final size:24
Alignment explanation
Indices: 844--947 Score: 63
Period size: 24 Copynumber: 4.3 Consensus size: 24
834 GAGATATTAG
*
844 AAATCA-AAACAGAATTC-AGAACAT
1 AAATCAGAAA-AGAATTCAAG-TCAT
* * * *
868 ATATCAGAACAGAATCCATA-TCAG
1 AAATCAGAAAAGAATTCA-AGTCAT
* *
892 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAAAAGAATTCAAGTCAT
**
916 GTATCAGAAAAGAATTCAAGTCGA-
1 AAATCAGAAAAGAATTCAAGTC-AT
940 AAATCAGA
1 AAATCAGA
948 TAAAATATTT
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
24 56 0.93
25 3 0.05
26 1 0.02
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.19
Consensus pattern (24 bp):
AAATCAGAAAAGAATTCAAGTCAT
Found at i:947 original size:48 final size:48
Alignment explanation
Indices: 837--930 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
827 GTAAAAGGAG
* * *
837 ATATTAGAAATCAAAACAGAATTCAGAACATATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACATATATCAGAAAAGAATCC
** *
885 ATATCAGAAATCAGAACAGAATTCAGGTCATGTATCAGAAAAGAAT
1 ATATCAGAAATCAGAACAGAATTCAGAACATATATCAGAAAAGAAT
931 TCAAGTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACATATATCAGAAAAGAATCC
Found at i:1616 original size:17 final size:18
Alignment explanation
Indices: 1594--1630 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1584 TCTTATGCAC
1594 ATCAAT-ATT-TTTATCAG
1 ATCAATAATTCTTT-TCAG
1611 ATCAATAATTCTTTTCAG
1 ATCAATAATTCTTTTCAG
1629 AT
1 AT
1631 TATTAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (18 bp):
ATCAATAATTCTTTTCAG
Found at i:1791 original size:34 final size:35
Alignment explanation
Indices: 1748--1813 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
1738 AATAAATTAT
*
1748 AATCTACATATCCTGGTTGATTCTTTT-TCACGTA
1 AATCTACATATCCTGGCTGATTCTTTTATCACGTA
*
1782 AATCTACATATCGTGGCTGATTCTTTTATCAC
1 AATCTACATATCCTGGCTGATTCTTTTATCAC
1814 TTAATTCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 25 0.86
35 4 0.14
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (35 bp):
AATCTACATATCCTGGCTGATTCTTTTATCACGTA
Found at i:2480 original size:31 final size:31
Alignment explanation
Indices: 2445--2511 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2435 TCAAAGTTTT
* *
2445 GGTCAACATGGTCACG-CCGGTCAACGGGTCG
1 GGTCAAC-GGGTCACGTCCGGTCAACGGGTCA
* *
2476 GGTCAACGGGTCAGGTCTGGTCAACGGGTCA
1 GGTCAACGGGTCACGTCCGGTCAACGGGTCA
2507 GGTCA
1 GGTCA
2512 GGTTATAACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.19, C:0.25, G:0.37, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCACGTCCGGTCAACGGGTCA
Found at i:2497 original size:18 final size:18
Alignment explanation
Indices: 2471--2510 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2461 CCGGTCAACG
2471 GGTCGGGTCAACGGGTCA
1 GGTCGGGTCAACGGGTCA
*
2489 GGTCTGGTCAACGGGTCA
1 GGTCGGGTCAACGGGTCA
2507 GGTC
1 GGTC
2511 AGGTTATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.42, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCA
Found at i:2511 original size:13 final size:13
Alignment explanation
Indices: 2463--2492 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2453 TGGTCACGCC
*
2463 GGTCAACGGGTCG
1 GGTCAACGGGTCA
2476 GGTCAACGGGTCA
1 GGTCAACGGGTCA
2489 GGTC
1 GGTC
2493 TGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:5291 original size:16 final size:16
Alignment explanation
Indices: 5270--5304 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5260 TCTGATTCAA
5270 CCTAACCAAGGATCAC
1 CCTAACCAAGGATCAC
5286 CCTAACCAAGGATCAC
1 CCTAACCAAGGATCAC
5302 CCT
1 CCT
5305 CCACATCGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.40, G:0.11, T:0.14
Consensus pattern (16 bp):
CCTAACCAAGGATCAC
Found at i:6149 original size:16 final size:17
Alignment explanation
Indices: 6128--6159 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6118 ATGTTGGACC
6128 GGGTCGGG-TCGGGCAG
1 GGGTCGGGTTCGGGCAG
6144 GGGTCGGGTTCGGGCA
1 GGGTCGGGTTCGGGCA
6160 AGATCTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.06, C:0.19, G:0.59, T:0.16
Consensus pattern (17 bp):
GGGTCGGGTTCGGGCAG
Found at i:6205 original size:24 final size:24
Alignment explanation
Indices: 6178--6232 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
6168 AAACCACCAC
6178 GCGGTGGGACTTCCCCACGCCCAG
1 GCGGTGGGACTTCCCCACGCCCAG
* *
6202 GCGGTGGGACTTCTCCATGCCCAG
1 GCGGTGGGACTTCCCCACGCCCAG
*
6226 ACGGTGG
1 GCGGTGG
6233 CACGTCCGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.35, G:0.36, T:0.16
Consensus pattern (24 bp):
GCGGTGGGACTTCCCCACGCCCAG
Found at i:9175 original size:29 final size:29
Alignment explanation
Indices: 9111--9207 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
9101 CCCGACTCGA
9111 TGACATTTTGGGAATTATTTTAAAAAATG
1 TGACATTTTGGGAATTATTTTAAAAAATG
* *
9140 TGGCATTTTGGGAATTCTTTT-AAAAATAG
1 TGACATTTTGGGAATTATTTTAAAAAAT-G
* * * *
9169 TGACATTATGGTAATTATTTTTAATAAAGG
1 TGACATTTTGGGAATTA-TTTTAAAAAATG
*
9199 TGATATTTT
1 TGACATTTT
9208 TGTAATTTTC
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
28 6 0.11
29 33 0.60
30 12 0.22
31 4 0.07
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTAAAAAATG
Found at i:14611 original size:19 final size:19
Alignment explanation
Indices: 14587--14652 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
14577 TAATTTGGAA
14587 GGATTTAATATGAATCATT
1 GGATTTAATATGAATCATT
* *
14606 GGATTTAAGATGAGTCATT
1 GGATTTAATATGAATCATT
* *
14625 -CATGTCAAATATGAATCATT
1 GGAT-T-TAATATGAATCATT
14645 GGATTTAA
1 GGATTTAA
14653 GTGACTAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 2 0.06
19 20 0.56
20 12 0.33
21 2 0.06
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (19 bp):
GGATTTAATATGAATCATT
Found at i:20695 original size:20 final size:20
Alignment explanation
Indices: 20670--20708 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20660 AAAGACTTAA
*
20670 ACAGAAATGCAGAAGCAAAG
1 ACAGAAATGCAGAAACAAAG
20690 ACAGAAATGCAGAAACAAA
1 ACAGAAATGCAGAAACAAA
20709 TAAAACTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.21, T:0.05
Consensus pattern (20 bp):
ACAGAAATGCAGAAACAAAG
Found at i:21092 original size:12 final size:12
Alignment explanation
Indices: 21077--21119 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
21067 GTTTGTTTAG
21077 ATGTTCGCGAAC
1 ATGTTCGCGAAC
*** *
21089 ATGTTCGTTTAG
1 ATGTTCGCGAAC
21101 ATGTTCGCGAAC
1 ATGTTCGCGAAC
21113 ATGTTCG
1 ATGTTCG
21120 TTCAACGTTC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (12 bp):
ATGTTCGCGAAC
Found at i:21092 original size:24 final size:24
Alignment explanation
Indices: 21038--21117 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 24
21028 TAACATTTGT
* **
21038 GAACGTGTTTGTTTA-ATGTTCAT
1 GAACATGTTTGTTTAGATGTTCGC
*
21061 GAATATGTTTGTTTAGATGTTCGC
1 GAACATGTTTGTTTAGATGTTCGC
*
21085 GAACATGTTCGTTTAGATGTTCGC
1 GAACATGTTTGTTTAGATGTTCGC
21109 GAACATGTT
1 GAACATGTT
21118 CGTTCAACGT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
23 13 0.26
24 37 0.74
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (24 bp):
GAACATGTTTGTTTAGATGTTCGC
Found at i:26944 original size:16 final size:16
Alignment explanation
Indices: 26923--26953 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26913 TGTGTATGTT
*
26923 GTGTTTGATAAGCATA
1 GTGTTTGAAAAGCATA
26939 GTGTTTGAAAAGCAT
1 GTGTTTGAAAAGCAT
26954 GGTTATAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (16 bp):
GTGTTTGAAAAGCATA
Found at i:31541 original size:17 final size:18
Alignment explanation
Indices: 31521--31554 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31511 ATCCTTTATA
31521 TCTT-GAATAGGCACAAG
1 TCTTGGAATAGGCACAAG
*
31538 TCTTGGAATAGTCACAA
1 TCTTGGAATAGGCACAA
31555 TTGCATAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (18 bp):
TCTTGGAATAGGCACAAG
Found at i:31828 original size:20 final size:20
Alignment explanation
Indices: 31805--31846 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
31795 TTATGAATAA
31805 TGAACAGTACCCGTGAACAG
1 TGAACAGTACCCGTGAACAG
31825 TGAACAGTACCCGTGAACAG
1 TGAACAGTACCCGTGAACAG
31845 TG
1 TG
31847 GGGGAATCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (20 bp):
TGAACAGTACCCGTGAACAG
Found at i:31883 original size:21 final size:20
Alignment explanation
Indices: 31845--31885 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31835 CCGTGAACAG
*
31845 TGGGGGAATCAGTTCCCATA
1 TGGGGGAATCAGTCCCCATA
*
31865 TGGGGGAATCGGTACCCCATA
1 TGGGGGAATCAGT-CCCCATA
31886 AGCATTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (20 bp):
TGGGGGAATCAGTCCCCATA
Found at i:32313 original size:46 final size:45
Alignment explanation
Indices: 32263--32388 Score: 146
Period size: 45 Copynumber: 2.8 Consensus size: 45
32253 ATCCAATATT
32263 TTACCATTTATTTCCATAAGCTCGTAAGCTTATTTTACCAAAATAA
1 TTACCATTTA-TTCCATAAGCTCGTAAGCTTATTTTACCAAAATAA
*** * * *
32309 TTACCATTTGCCCCATAAGCTCGTAAGCTTATTTTTACCCATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTA-TTTTACCAAAATAA
* * *
32355 TTGCCA-ATATTCCATAAGCTCATAAGCTTATTTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
32389 CATGCTTACC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 4 0.06
45 38 0.57
46 25 0.37
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAA
Found at i:32536 original size:40 final size:40
Alignment explanation
Indices: 32492--32653 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
32482 ACCGTAGTGC
32492 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
32532 TACACATAAGGTCGTGCCTACCATGTACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
32572 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
32612 TACACATAAGGTCGTGCCCACCATATACACCGAATTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
32652 TA
1 TA
32654 TAAACCTGAA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:38889 original size:20 final size:20
Alignment explanation
Indices: 38866--38905 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
38856 TTATGAATAA
*
38866 TGAACAGTACCCGTGAACAG
1 TGAACAATACCCGTGAACAG
38886 TGAACAATACCCGTGAACAG
1 TGAACAATACCCGTGAACAG
38906 CAGGGGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (20 bp):
TGAACAATACCCGTGAACAG
Found at i:39609 original size:40 final size:40
Alignment explanation
Indices: 39565--39726 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
39555 ACCGTAGTGC
39565 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
39605 TACACATAAGGTCGTGCCTACCATGTACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
39645 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
39685 TACACATAAGGTCGTGCCCACCATATACACCGAATTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
39725 TA
1 TA
39727 TAAACCTGAA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:45960 original size:20 final size:20
Alignment explanation
Indices: 45937--45976 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
45927 TTATGAATAA
*
45937 TGAACAGTACCCGTGAACAG
1 TGAACAATACCCGTGAACAG
45957 TGAACAATACCCGTGAACAG
1 TGAACAATACCCGTGAACAG
45977 CAGGGGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (20 bp):
TGAACAATACCCGTGAACAG
Found at i:46680 original size:40 final size:40
Alignment explanation
Indices: 46636--46717 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
46626 ACCGTAGTGC
46636 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
46676 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
46716 TA
1 TA
46718 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:54191 original size:24 final size:24
Alignment explanation
Indices: 54143--54191 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54133 TATTTTATCT
* * *
54143 TTGTTTTAGGTATTTTAGTTTAAA
1 TTGTTTTAAGTATTTTAATTAAAA
*
54167 TTGTTTTAAGTGTTTTAATTAAAA
1 TTGTTTTAAGTATTTTAATTAAAA
54191 T
1 T
54192 AATGATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (24 bp):
TTGTTTTAAGTATTTTAATTAAAA
Found at i:54710 original size:18 final size:18
Alignment explanation
Indices: 54687--54729 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
54677 CTTTAGATTA
*
54687 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
54705 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
54723 TTTATTT
1 TTTATTT
54730 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:54816 original size:16 final size:16
Alignment explanation
Indices: 54798--54827 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54788 TATTTCCCTT
54798 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
54813 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
54828 CCCACATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:55639 original size:17 final size:17
Alignment explanation
Indices: 55619--55660 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
55609 GAAAGCGACG
55619 CCTTCGTGAAAATTTAT
1 CCTTCGTGAAAATTTAT
55636 CCTTCGTGAAAATTTAT
1 CCTTCGTGAAAATTTAT
*
55653 TCTTCGTG
1 CCTTCGTG
55661 TGGGCCTAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (17 bp):
CCTTCGTGAAAATTTAT
Found at i:58579 original size:15 final size:15
Alignment explanation
Indices: 58556--58595 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
58546 GAACAAAAAT
*
58556 CAAAAAGAAAATAAA
1 CAAAGAGAAAATAAA
58571 CAAAGAGAAAATAAA
1 CAAAGAGAAAATAAA
58586 CAAAGA-AAAA
1 CAAAGAGAAAA
58596 GGGTCAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.78, C:0.07, G:0.10, T:0.05
Consensus pattern (15 bp):
CAAAGAGAAAATAAA
Found at i:59657 original size:32 final size:32
Alignment explanation
Indices: 59621--59705 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 32
59611 AGGAAGAGTG
* *
59621 GGGGCATCTTTGAAGATTCAAAATCAAATGTT
1 GGGGCATCTTTGGAGATTCAAAATCAAATATT
* * * *
59653 GGGGCATTTTTGGATATTCAACATCGAATATT
1 GGGGCATCTTTGGAGATTCAAAATCAAATATT
** *
59685 GTTGCATCTTTGGGGATTCAA
1 GGGGCATCTTTGGAGATTCAA
59706 CATCCTGATA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (32 bp):
GGGGCATCTTTGGAGATTCAAAATCAAATATT
Found at i:61723 original size:18 final size:18
Alignment explanation
Indices: 61700--61742 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
61690 CCTTAGATTA
*
61700 TTTATTTAATTATTTTCC
1 TTTATTTAATTATTATCC
* *
61718 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCC
61736 TTTATTT
1 TTTATTT
61743 TAAAAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCC
Found at i:61830 original size:16 final size:16
Alignment explanation
Indices: 61812--61841 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61802 TATTTCCTTT
61812 TTTTATC-TTATTTTG
1 TTTTATCTTTATTTTG
61827 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
61842 CCCACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:61888 original size:19 final size:18
Alignment explanation
Indices: 61848--61888 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
61838 TTTTCCCACT
* *
61848 TTTTTATTTTATTTTGTT
1 TTTTTATTTTATTTTCTC
61866 TTTTTACTTTTATTTTCTC
1 TTTTTA-TTTTATTTTCTC
61885 TTTT
1 TTTT
61889 AACATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTATTTTATTTTCTC
Found at i:61896 original size:20 final size:20
Alignment explanation
Indices: 61853--61896 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
61843 CCACTTTTTT
* * *
61853 ATTTTATTTTGTTTTTTTAC
1 ATTTTATTTTCTCTTTTAAC
61873 -TTTTATTTTCTCTTTTAAC
1 ATTTTATTTTCTCTTTTAAC
61892 ATTTT
1 ATTTT
61897 TTATATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (20 bp):
ATTTTATTTTCTCTTTTAAC
Found at i:66967 original size:56 final size:56
Alignment explanation
Indices: 66876--66983 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 56
66866 AATTCATGTG
*
66876 AAAACATCCTACCCGAAGGTCTCATGGATGGCCCGAAGGACTTATCATCTTGGTGC
1 AAAACATCCTACCCGAAGGTCTCATGGATGACCCGAAGGACTTATCATCTTGGTGC
* * * *
66932 AAAACATCCTGCCCTAAGGTCTTATGGATGACCCGAAGGATTTATCATCTTG
1 AAAACATCCTACCCGAAGGTCTCATGGATGACCCGAAGGACTTATCATCTTG
66984 TTCGAGAGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (56 bp):
AAAACATCCTACCCGAAGGTCTCATGGATGACCCGAAGGACTTATCATCTTGGTGC
Found at i:67304 original size:215 final size:215
Alignment explanation
Indices: 66932--67338 Score: 568
Period size: 215 Copynumber: 1.9 Consensus size: 215
66922 ATCTTGGTGC
* * * * * *
66932 AAAACATCCTGCCCTAAGGTCTTATGGATGACCCGAAGGATTTATCATCTTGTTCGAGAGACGCA
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAAGACTTATCATCTTGCTCGAAAGACGCA
* * *
66997 CAAATGACCCGAACGATTTTAAGCATAGTGCTCGAAAGACTTACTGATGGCCCGAATGACTTATA
66 CAAATGACCCGAACGATTTTAAGCATAGTGCTCGAAAGACTTACTAATGGACCGAAGGACTTATA
67062 AATTATGAAATTTTGAAAATCGCATTCTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCATTT
131 AATTATGAAATTTTGAAAATCGCATTCTTCGTTTTAAAAAATTCCATCTT-TTAAAACATCATTT
67127 TTTCATTTTCAAATTCATGTG
195 TTTCATTTTCAAATTCATGTG
* * * * **
67148 AAAACATTCTACCCGAAGGTTTTATGGAT-AGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTT
1 AAAACATCCTACCCGAAGGTCTTATGGATGA-CCCGAAAGACTTATCATCTTGCTCGAAAGACGC
* *
67212 ACAGATGACCCGAATGA-TTTAAGCATCA-TGCTCGAAAGACTTACTAATGGACCGAAGGACTTA
65 ACAAATGACCCGAACGATTTTAAGCAT-AGTGCTCGAAAGACTTACTAATGGACCGAAGGACTTA
* * * * *
67275 TAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTTCATCTTTTTAAACATCAT
129 TAAATTATGAAATTTTGAAAATCGCATTCTTCGTTTTAAAAAATTCCATCTTTTAAAACATCAT
67339 ACCCGAAGGT
Statistics
Matches: 167, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
214 11 0.07
215 90 0.54
216 66 0.40
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (215 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAAGACTTATCATCTTGCTCGAAAGACGCA
CAAATGACCCGAACGATTTTAAGCATAGTGCTCGAAAGACTTACTAATGGACCGAAGGACTTATA
AATTATGAAATTTTGAAAATCGCATTCTTCGTTTTAAAAAATTCCATCTTTTAAAACATCATTTT
TTCATTTTCAAATTCATGTG
Found at i:67436 original size:42 final size:41
Alignment explanation
Indices: 67360--67455 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
67350 TTATGGATTG
* * * *
67360 CCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAAATGA
1 CCCGAAGGACTTAGCATCATGCTCGAAAGACTTACAAATGA
* ** *
67401 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACAAATGA
67443 CCCGAAGGACTTA
1 CCCGAAGGACTTA
67456 TAAACTGTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 12 0.27
42 33 0.73
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (41 bp):
CCCGAAGGACTTAGCATCATGCTCGAAAGACTTACAAATGA
Found at i:67467 original size:181 final size:182
Alignment explanation
Indices: 67148--67519 Score: 613
Period size: 181 Copynumber: 2.0 Consensus size: 182
67138 AATTCATGTG
67148 AAAACATTC-TACCCGAAGGTTTTATGGATAGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTT
1 AAAACA-TCATACCCGAAGGTTTTATGGATAGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTT
* *
67212 ACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTAATGGACCGAAGGACTTATA
65 ACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGACCGAAGGACTTATA
* ** *
67277 AATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTTCATCTT-TT
130 AACTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTT
* * *
67329 TAAACATCATACCCGAAGGTTTTATGGATTGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCATACCCGAAGGTTTTATGGATAGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTTA
* *
67394 CAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGACCGAAGGACTTATAA
*
67459 ACTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAACTTCCATCTTCTT
131 ACTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTT
67511 AAAACATCA
1 AAAACATCA
67520 CTTTTCATTT
Statistics
Matches: 176, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
180 2 0.01
181 164 0.93
182 10 0.06
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (182 bp):
AAAACATCATACCCGAAGGTTTTATGGATAGCCCGAAAGACTTATCATCTTGCTCTAAAGGCTTA
CAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGGACCGAAGGACTTATAA
ACTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTCCATCTTCTT
Found at i:67700 original size:214 final size:214
Alignment explanation
Indices: 67340--67797 Score: 776
Period size: 214 Copynumber: 2.1 Consensus size: 214
67330 AAACATCATA
67340 CCCGAAGGTTTTATGGATTGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCG
1 CCCGAAGGTTTTATGGA-TGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCG
67405 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAACTGTGAAATT
65 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAACTGTGAAATT
*
67470 TTGAAAATCACATTCTTCGTTTTC-AAAACTTCCATCTTCTTAAAACATCAC-TTTTCATTTTCA
130 TTGAAAATCACATTCTTCGTTTTCAAAAAATT-CATCTTCTTAAAACATCACTTTTTCATTTTCA
67533 AATTCATTTGAAAACATCCCT
194 AATTCATTTGAAAACATCCCT
* *
67554 CCCGAAGGTTTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGAGCCG
1 CCCGAAGGTTTTATGGATG-CCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCG
* * * *
67619 AAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCTGAGGGACTTATAAATTGTGAAATT
65 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAACTGTGAAATT
**
67684 TTGAAAATTGCATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCACTTTTTCATTTTCAA
130 TTGAAAATCACATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCACTTTTTCATTTTCAA
67749 ATTCATTTGAAAACATCCCT
195 ATTCATTTGAAAACATCCCT
*
67769 CCCGAAGGTCTTATGGATGGCCCGAAGGA
1 CCCGAAGGTTTTATGGAT-GCCCGAAGGA
67798 TTTAAACATC
Statistics
Matches: 230, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
213 2 0.01
214 162 0.70
215 65 0.28
216 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (214 bp):
CCCGAAGGTTTTATGGATGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAAATGACCCGA
AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAACTGTGAAATTT
TGAAAATCACATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCACTTTTTCATTTTCAAA
TTCATTTGAAAACATCCCT
Found at i:67902 original size:170 final size:173
Alignment explanation
Indices: 67616--67993 Score: 543
Period size: 170 Copynumber: 2.2 Consensus size: 173
67606 TACAGATGAG
* * *
67616 CCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCTGAGGGACTTATAAATTGTGAA
1 CCGAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGGCCCGAGGGAC-TAT-AATTATGAA
* **
67681 ATTTTGAAAATTGCATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCA-CTTTTTCATTT
64 ATTTTAAAAATCACATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCATCTTTTTCATTT
***
67745 TCAAATTCATTTGAAAACATCCCT-CCCGAAGGTCTTATGGATGGC
129 TCAAATTCATTTGAAAACAT-CCTACCCGAAAACCTTATGGATGGC
67790 CCGAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGGCCCGAGGGA-TAT-ATTATGAAAT
1 CCGAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGGCCCGAGGGACTATAATTATGAAAT
*
67853 TTTAAAAATCACATTCTTCGTTTTC-AAAAATTCCATCTTCTTAAAACATCATTTTTTTCATTTT
66 TTTAAAAATCACATTCTTCGTTTTCAAAAAATT-CATCTTCTTAAAACATCATCTTTTTCATTTT
67917 CAAATTCATTTGAAAACATCCTACCCGAAAACCTTATGGATGGC
130 CAAATTCATTTGAAAACATCCTACCCGAAAACCTTATGGATGGC
* * * * *
67961 CCAAAGGACTT-ATCATCTTGCTCTAAAGACTTA
1 CCGAAGGATTTAAACATCATGCTCGAAAGACTTA
67994 CAGATGACCC
Statistics
Matches: 186, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
169 7 0.04
170 71 0.38
171 57 0.31
172 3 0.02
174 48 0.26
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (173 bp):
CCGAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGGCCCGAGGGACTATAATTATGAAAT
TTTAAAAATCACATTCTTCGTTTTCAAAAAATTCATCTTCTTAAAACATCATCTTTTTCATTTTC
AAATTCATTTGAAAACATCCTACCCGAAAACCTTATGGATGGC
Found at i:68149 original size:206 final size:208
Alignment explanation
Indices: 67784--68366 Score: 659
Period size: 206 Copynumber: 2.8 Consensus size: 208
67774 AGGTCTTATG
* * * * * * * *
67784 GATGGCCCGAAGGATTTAAACATCATGCTCGAAAGACTTATTGATGG-CCCGAGGGA--TAT--A
1 GATGACCCGAAGGATTTAAGCATCATGATCGAAAAACTTACTAATGGCCCCAAAGGACTTATAAA
* *
67844 TTATGAAATTTTAAAAATCACATTCTTCGTTTTCAAAA-ATTCCATCTTCTTAAAACATCATTTT
66 TTATGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAGATT-CA----C----ATCATCA-TTT
*
67908 TTTCATTTTCAAATTCATTTGAAAACATCCTACCCGAAAACCTTATGGATGGCCC-AAAGGACTT
121 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAAACCTTATGGATGGCCCGAAA-GACTT
67972 ATCATCTTGCTCTAAAGACTTACA
185 ATCATCTTGCTCTAAAGACTTACA
* *
67996 GATGACCCGAAGGATTTAAGCATCATGATC-AAAAGACTTAC-AGATGG-CTCGAAGGACTTATA
1 GATGACCCGAAGGATTTAAGCATCATGATCGAAAA-ACTTACTA-ATGGCCCCAAAGGACTTATA
* * *
68058 AATTGTGAAAATTTTGAAAATCGCATTCTTTGTTTTCAAAA-ATTC-CATCATCATTTTTTCATT
64 AATTATG-AAATTTTAAAAATCGCATTCTTCGTTTTCAAAAGATTCACATCATCATTTTTTCATT
* ****
68121 TTCAATTTCATGTGAAAACATCCTACCCGAAGGTTTTATGGATGGCCCGAAAGACTTATCATCTT
128 TTCAAATTCATGTGAAAACATCCTACCCGAAAACCTTATGGATGGCCCGAAAGACTTATCATCTT
*
68186 GCTCTAAAGGCTTACA
193 GCTCTAAAGACTTACA
*
68202 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAAACTTACTAATGGCCCCAAAGGACTTATAAA
1 GATGACCCGAAGGATTTAAGCATCATGATCGAAAAACTTACTAATGGCCCCAAAGGACTTATAAA
* * *
68267 TTATGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAGTTTCATCTTCTTAAAACATCATTTTT
66 TTATGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAGATTCA-CATC----ATCAT--TTTTT
68332 CATTTTCAAATTCATGTGAAAACATCCTACCCGAA
124 CATTTTCAAATTCATGTGAAAACATCCTACCCGAA
68367 GGTCTTATAG
Statistics
Matches: 321, Mismatches: 30, Indels: 37
0.83 0.08 0.10
Matches are distributed among these distances:
206 150 0.47
207 36 0.11
209 3 0.01
211 4 0.01
212 43 0.13
213 4 0.01
214 3 0.01
215 39 0.12
216 6 0.02
217 33 0.10
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (208 bp):
GATGACCCGAAGGATTTAAGCATCATGATCGAAAAACTTACTAATGGCCCCAAAGGACTTATAAA
TTATGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAGATTCACATCATCATTTTTTCATTTTC
AAATTCATGTGAAAACATCCTACCCGAAAACCTTATGGATGGCCCGAAAGACTTATCATCTTGCT
CTAAAGACTTACA
Found at i:68430 original size:34 final size:34
Alignment explanation
Indices: 68386--68761 Score: 441
Period size: 34 Copynumber: 10.9 Consensus size: 34
68376 GATGGATTTA
*
68386 CTTCACTACTCTTCGGTGAAGGCTTAAGATGGTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGGTG
* * *
68420 CTTCATTACTCCTCTGTGAAGGCTTAAGTTGGTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGGTG
* **
68454 CTTCATTACTCCCCTGTGAAGGCTTAAGATGGTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGGTG
*
68488 CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATG-GTG
* * * *
68523 TTTCACTACTCTCCGGTGAAGGATTAAGATGGTTTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGG--TG
* *
68559 CTTCACTACTCCTCCGTGAAGGCTTAAGATGGTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGGTG
* * *
68593 CTTTACTACTCTTCTGTGAAGGCTTAAGAAGATTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATG-GTG
* * *
68628 CCTCACTACTCTCCGGTGAAGGC-TAAGATGGTTTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGG--TG
*
68663 CTTCACTACTCCTCTGTGAAGGCTTAAGATGGTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGGTG
* * *
68697 CTTCACTACACTTTTGTGAAGGCTTAAGATGATTG
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATG-GTG
*
68732 CTTCAGTACTC-TCTGATGAAGGCTTAAGAT
1 CTTCACTACTCTTCTG-TGAAGGCTTAAGAT
68762 TGACTTTGCT
Statistics
Matches: 291, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
34 158 0.54
35 96 0.33
36 37 0.13
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (34 bp):
CTTCACTACTCTTCTGTGAAGGCTTAAGATGGTG
Found at i:68584 original size:105 final size:105
Alignment explanation
Indices: 68386--68761 Score: 539
Period size: 104 Copynumber: 3.6 Consensus size: 105
68376 GATGGATTTA
* * * * *
68386 CTTCACTACTCTTCGGTGAAGGCTTAAGATG-GTGCTTCATTACTC-CTCTGTGAAGGCTTAAGT
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTGCTTCACTACTCTC-CGGTGAAGGCTTAAGA
*
68449 TGG--TGCTTCATTACTCC-CCTGTGAAGGCTTAAGATGGTG
65 TGGTTTGCTTCACTACTCCTCC-GTGAAGGCTTAAGATGGTG
* *
68488 CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTGTTTCACTACTCTCCGGTGAAGGATTAAGAT
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTGCTTCACTACTCTCCGGTGAAGGCTTAAGAT
68553 GGTTTGCTTCACTACTCCTCCGTGAAGGCTTAAGATGGTG
66 GGTTTGCTTCACTACTCCTCCGTGAAGGCTTAAGATGGTG
* * *
68593 CTTTACTACTCTTCTGTGAAGGCTTAAGAAGATTGCCTCACTACTCTCCGGTGAAGGC-TAAGAT
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTGCTTCACTACTCTCCGGTGAAGGCTTAAGAT
*
68657 GGTTTGCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTG
66 GGTTTGCTTCACTACTCCTCCGTGAAGGCTTAAGATGGTG
* * * * *
68697 CTTCACTACACTTTTGTGAAGGCTTAAGATGATTGCTTCAGTACTCTCTGATGAAGGCTTAAGAT
1 CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTGCTTCACTACTCTCCGGTGAAGGCTTAAGAT
68762 TGACTTTGCT
Statistics
Matches: 246, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
102 30 0.12
103 27 0.11
104 96 0.39
105 91 0.37
106 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (105 bp):
CTTCACTACTCTTCTGTGAAGGCTTAAGATGATTGCTTCACTACTCTCCGGTGAAGGCTTAAGAT
GGTTTGCTTCACTACTCCTCCGTGAAGGCTTAAGATGGTG
Found at i:70955 original size:13 final size:13
Alignment explanation
Indices: 70939--70974 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
70929 ATTTTCAATT
70939 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
*
70952 TTTTCTTTTTTTC
1 TTTTCTTTCTTTC
*
70965 TTCTCTTTCT
1 TTTTCTTTCT
70975 ACATTTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:70955 original size:22 final size:22
Alignment explanation
Indices: 70930--70974 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
70920 ATTTTTCTCA
70930 TTTTCAATTTTTTCTT-TCTTTC
1 TTTTC-ATTTTTTCTTCTCTTTC
*
70952 TTTTCTTTTTTTCTTCTCTTTC
1 TTTTCATTTTTTCTTCTCTTTC
70974 T
1 T
70975 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCATTTTTTCTTCTCTTTC
Found at i:70973 original size:17 final size:18
Alignment explanation
Indices: 70939--70991 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
70929 ATTTTCAATT
70939 TTTTCTTTCTTTCTTTTC
1 TTTTCTTTCTTTCTTTTC
70957 TTTT-TTTCTTCTCTTTCTAC
1 TTTTCTTTCTT-TCTTT-T-C
*
70977 ATTTCTCTTCTTTCT
1 TTTTCT-TTCTTTCT
70992 CCTCATGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 1 0.03
20 4 0.14
21 4 0.14
22 5 0.17
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTCTTTCTTTCTTTTC
Found at i:82324 original size:240 final size:240
Alignment explanation
Indices: 81881--82328 Score: 575
Period size: 241 Copynumber: 1.9 Consensus size: 240
81871 GATTGTGATG
* *
81881 TGAGTTAAGCTAAATTGTTGATGACTCATTCATCGTGAAGTTGAGTCGATCTCAGATACTTCAAG
1 TGAGTTAAGCTAAATTGTGGATGACTCATTCATCGAGAAGTTGAGTCGATCTCAGATACTTCAAG
* * * ** * * *
81946 ATGATATCCTTCGTTGTGAAATTGAAATCTAGCTTAAAGTTTGGGTTGGGAAGTAGCTCCTCATC
66 ATGATATCCTTCGTCGTGAAATTGAAATCTAGCTTAAAGTCTAGACTGGGAAATAACTCCTCATA
* * * **
82011 TTTGACTTAAGCTAAATCGCAATTGATTTTCGATCTTCTTCTAGTCCAATATCCTTTTTTCGTGA
131 GTTGACTTAAGCTAAATCGCAATTGATTTTCGATCTTCTTCTACTCCAATATCCATTCGTCGTGA
*
82076 AGTTAAAATTTGAATCGAAGTTCGTAAAAAATAGCTCCTCATTGT
196 AATTAAAATTTGAATCGAAGTTCGTAAAAAATAGCTCCTCATTGT
* ** *
82121 TGAGTTAAGCTAAATTGTGGATGACTCATTCGTCGAGAAGTTGAGTCGATCTTGGATGACTT-GA
1 TGAGTTAAGCTAAATTGTGGATGACTCATTCATCGAGAAGTTGAGTCGATCTCAGAT-ACTTCAA
* *
82185 GCATGATATCCTTCGTCGTGAAGTTGAAATCTAG-TCTGAAGTCTAGACTGGGAAATAACTCCTT
65 G-ATGATATCCTTCGTCGTGAAATTGAAATCTAGCT-TAAAGTCTAGACTGGGAAATAACTCC-T
* * *
82249 CA-AGTTGAGTTAAGCTGAATC-CTAGTTGATTTTC-ATTCTTCTTCTACTCCAATAT-CATTCG
127 CATAGTTGACTTAAGCTAAATCGC-AATTGATTTTCGA-TCTTCTTCTACTCCAATATCCATTCG
82310 TCGTGAAATTAAAATTTGA
190 TCGTGAAATTAAAATTTGA
82329 CTTGAAGACC
Statistics
Matches: 177, Mismatches: 25, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
240 78 0.44
241 96 0.54
242 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (240 bp):
TGAGTTAAGCTAAATTGTGGATGACTCATTCATCGAGAAGTTGAGTCGATCTCAGATACTTCAAG
ATGATATCCTTCGTCGTGAAATTGAAATCTAGCTTAAAGTCTAGACTGGGAAATAACTCCTCATA
GTTGACTTAAGCTAAATCGCAATTGATTTTCGATCTTCTTCTACTCCAATATCCATTCGTCGTGA
AATTAAAATTTGAATCGAAGTTCGTAAAAAATAGCTCCTCATTGT
Done.