Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006036.1 Hibiscus syriacus cultivar Beakdansim tig00014253_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: 82362
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2916 original size:21 final size:21
Alignment explanation
Indices: 2890--2929 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2880 CCCCCTTTGA
*
2890 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2911 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2930 TGGGGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:7130 original size:21 final size:19
Alignment explanation
Indices: 7104--7145 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
7094 ATACCCACAG
*
7104 CAGTATCTATATTAGTTGCAT
1 CAGTATCGATATT-GTT-CAT
7125 CAGTATCGATATTGTTCAT
1 CAGTATCGATATTGTTCAT
7144 CA
1 CA
7146 TATTTCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 12 0.60
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (19 bp):
CAGTATCGATATTGTTCAT
Found at i:11587 original size:19 final size:18
Alignment explanation
Indices: 11563--11646 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 18
11553 TATGAAATTA
11563 TTTTAAAATATATATTAAT
1 TTTTAAAATA-ATATTAAT
*
11582 TTTTAAAATAATATTATT
1 TTTTAAAATAATATTAAT
*
11600 TATTTGAAATAATATTAATTAT
1 T-TTTAAAATAATATT-A--AT
*
11622 TATTTTAAATAATATT-AT
1 T-TTTAAAATAATATTAAT
11640 TTTTAAA
1 TTTTAAA
11647 TTATCTATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.09
18 11 0.20
19 23 0.41
20 1 0.02
22 16 0.29
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
TTTTAAAATAATATTAAT
Found at i:11613 original size:22 final size:22
Alignment explanation
Indices: 11588--11644 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
11578 TAATTTTTAA
*
11588 AATAATATTATTTATTTGAAAT
1 AATATTATTATTTATTTGAAAT
*
11610 AATATTAATTA-TTATTTTAAAT
1 AATATT-ATTATTTATTTGAAAT
11632 AATATTATT-TTTA
1 AATATTATTATTTA
11645 AATTATCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 6 0.19
22 21 0.68
23 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AATATTATTATTTATTTGAAAT
Found at i:11634 original size:16 final size:16
Alignment explanation
Indices: 11615--11670 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
11605 GAAATAATAT
11615 TAATTATTATTTTAAA
1 TAATTATTATTTTAAA
11631 TAA-TATTATTTTTAAA
1 TAATTATTA-TTTTAAA
* *
11647 TTATCTATTTAAGTTTAAA
1 TAAT-TA-TT-ATTTTAAA
11666 TAATT
1 TAATT
11671 GTATGAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 5 0.16
16 12 0.38
18 3 0.09
19 11 0.34
20 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TAATTATTATTTTAAA
Found at i:30905 original size:10 final size:10
Alignment explanation
Indices: 30890--30914 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
30880 GCTAAATTGA
30890 AAAAAAAATT
1 AAAAAAAATT
30900 AAAAAAAATT
1 AAAAAAAATT
30910 AAAAA
1 AAAAA
30915 TTTAATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:31952 original size:11 final size:11
Alignment explanation
Indices: 31936--31966 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
31926 GTAGGGCTAG
31936 GGTTAGGTTCA
1 GGTTAGGTTCA
31947 GGTTAGGTTCA
1 GGTTAGGTTCA
31958 GGTTAGGTT
1 GGTTAGGTT
31967 TTAATTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.06, G:0.39, T:0.39
Consensus pattern (11 bp):
GGTTAGGTTCA
Found at i:32546 original size:91 final size:91
Alignment explanation
Indices: 32382--32555 Score: 235
Period size: 91 Copynumber: 1.9 Consensus size: 91
32372 TGAGCTAAGG
* *
32382 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTTTCATTATGATC
1 TTGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTATTTTCATTATGAAC
*
32447 CCTCCACTGGAAATGTTGTGCCAAGT
66 CCTCCACTGAAAATGTTGTGCCAAGT
* * **
32473 TTGAACAAGTTCTTCTCTTTATGATA-TTATTCTCCCTCGTTGGATTTGTT-TTTGTCATTATGA
1 TTGAACAAGCTCTTCTCATTATGA-ACTTATTCTCCCTCGTTGGATGAGTTATTT-TCATTATGA
* *
32536 ACTCTGCACTGAAAATGTTG
64 ACCCTCCACTGAAAATGTTG
32556 AGTGCTTTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
90 3 0.04
91 68 0.94
92 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (91 bp):
TTGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTATTTTCATTATGAAC
CCTCCACTGAAAATGTTGTGCCAAGT
Found at i:33612 original size:12 final size:12
Alignment explanation
Indices: 33595--33636 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
33585 TCTTGGACCC
33595 TCATTTTTATTT
1 TCATTTTTATTT
33607 TCATTTTTCATTT
1 TCATTTTT-ATTT
33620 TC-TTTTTA-TT
1 TCATTTTTATTT
33630 TCATTTT
1 TCATTTT
33637 CTTTTCCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 5 0.18
12 13 0.46
13 6 0.21
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (12 bp):
TCATTTTTATTT
Found at i:38799 original size:23 final size:22
Alignment explanation
Indices: 38769--38850 Score: 101
Period size: 23 Copynumber: 3.6 Consensus size: 22
38759 ATGTTTCCCA
* **
38769 AAGGACCATATAGGGTTGTCCAG
1 AAGGACCACATAGTTTTGTCC-G
38792 AAGGACCACATAGTTTTGTGCCG
1 AAGGACCACATAGTTTTGT-CCG
*
38815 AAGGAACACATAGTTTTGTCCTG
1 AAGGACCACATAGTTTTGTCC-G
38838 AAGGACCACATAG
1 AAGGACCACATAG
38851 AACCCTCGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
22 2 0.04
23 48 0.92
24 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (22 bp):
AAGGACCACATAGTTTTGTCCG
Found at i:41047 original size:46 final size:46
Alignment explanation
Indices: 40870--41320 Score: 448
Period size: 46 Copynumber: 9.8 Consensus size: 46
40860 TTATTCGTTA
* * * *
40870 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCCGTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
40916 ATATTTAGTTATGGCATTCTTTCATGCCTTAATGCATCCGTTCATGC
1 AT-TTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * *
40963 ATATTTAGTTGTGACATCATTTCATGCCTTAATACATCCTTTCATGC
1 AT-TTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
41010 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGG
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
41056 ATTTCAGTTATGGCATCCTTTCATGACTTAATGCATCCGTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
41102 ATTTTTAGTTATGGCATCCTTTCATGCATTAATGCATCTTTTCATGC
1 A-TTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
41149 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCAT-CTATTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCT-TTCATGC
* * ** **
41195 ATTTCAGTTATGACATCCTTTCATACAAATAATGCA-CCCAT-ATGC
1 ATTTCAGTTATGGCATCCTTTCATGC-CTTAATGCATCCTTTCATGC
* * * **
41240 ATTATTA-TTTTGGCATCCTTTCATGCCAATAATGCA-CCCAT-ATGC
1 ATT-TCAGTTATGGCATCCTTTCATGCC-TTAATGCATCCTTTCATGC
* * *
41285 ATTATTA-TTTTGGCATCCTTTCATGCCGATAATGCA
1 ATT-TCAGTTATGGCATCCTTTCATGCC-TTAATGCA
41321 CCCATATGCA
Statistics
Matches: 354, Mismatches: 44, Indels: 15
0.86 0.11 0.04
Matches are distributed among these distances:
45 76 0.21
46 147 0.42
47 131 0.37
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (46 bp):
ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:41125 original size:139 final size:139
Alignment explanation
Indices: 40870--41310 Score: 538
Period size: 139 Copynumber: 3.2 Consensus size: 139
40860 TTATTCGTTA
* * * *
40870 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCCGTTCATGCATATTTAGTTATGGCATTC
1 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCATCCTTTCATGCAT-TTCAGTTATGGCATCC
* * * * *
40935 TTTCATGCCTTAATGCATCCGTTCATGCATATTTAGTTGTGACATCATTTCATGCCTTAATACAT
65 TTTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATACAT
41000 CCTTTCATGC
130 CCTTTCATGC
* * *
41010 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGGATTTCAGTTATGGCATCCT
1 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
* *
41075 TTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCATTAATGCATC
66 TTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATACATC
*
41140 TTTTCATGC
131 CTTTCATGC
*
41149 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCAT-CTATTCATGCATTTCAGTTATGACATCC
1 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCATCCT-TTCATGCATTTCAGTTATGGCATCC
* ** * * * *
41213 TTTCAT-ACAAATAATGCA-CCCAT-ATGCATTATTA-TTTTGGCATCCTTTCATGCCAATAATG
65 TTTCATGAC--TTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCC-TTAATA
**
41274 CA-CCCAT-ATGC
127 CATCCTTTCATGC
*
41285 ATTATTATTT-TGGCATCCTTTCATGC
1 ATT-TCATTTATGGCATCCTTTCATGC
41311 CGATAATGCA
Statistics
Matches: 266, Mismatches: 30, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
136 23 0.09
137 25 0.09
138 21 0.08
139 147 0.55
140 50 0.19
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (139 bp):
ATTTCATTTATGGCATCCTTTCATGCTTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
TTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATACATC
CTTTCATGC
Found at i:41257 original size:45 final size:45
Alignment explanation
Indices: 41066--41338 Score: 241
Period size: 45 Copynumber: 6.0 Consensus size: 45
41056 ATTTCAGTTA
* * ** * *
41066 TGGCATCCTTTCATGAC-TTAATGCATCCGTTCATGCATTTTTAGTTA
1 TGGCATCCTTTCATGCCAATAATGCA-CCCAT-ATGCATTATTA-TTT
* *** *
41113 TGGCATCCTTTCATG-CATTAATGCATCTTTTCATGCATT-TCATTT
1 TGGCATCCTTTCATGCCAATAATGCA-CCCAT-ATGCATTATTATTT
** * * * *
41158 ATGGCATCCTTTCATG-CTTTAATGCATCTATTCATGCATT-TCAGTTA
1 -TGGCATCCTTTCATGCCAATAATGCACCCA-T-ATGCATTATTA-TTT
* * *
41205 TGACATCCTTTCATACAAATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
41250 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
*
41295 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATT
1 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATT
41339 CTGTTCATTC
Statistics
Matches: 198, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
45 97 0.49
46 55 0.28
47 46 0.23
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.41
Consensus pattern (45 bp):
TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
Found at i:41962 original size:22 final size:22
Alignment explanation
Indices: 41937--41990 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
41927 TAGATCCATG
41937 GTATCGATACATCCCTTTGTTA
1 GTATCGATACATCCCTTTGTTA
*
41959 GTATCGATACTTCCCTTTGTTA
1 GTATCGATACATCCCTTTGTTA
41981 GTATCGATAC
1 GTATCGATAC
41991 CCCTTCAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (22 bp):
GTATCGATACATCCCTTTGTTA
Found at i:44455 original size:4 final size:4
Alignment explanation
Indices: 44446--44494 Score: 71
Period size: 4 Copynumber: 12.2 Consensus size: 4
44436 TCCATGAAAG
* * *
44446 GTAT GTAT GTAT GCAT GCAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
44494 G
1 G
44495 AAATGGATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (4 bp):
GTAT
Found at i:44469 original size:12 final size:12
Alignment explanation
Indices: 44452--44513 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
44442 AAAGGTATGT
44452 ATGTATGCATGC
1 ATGTATGCATGC
*
44464 ATGTATGCATGT
1 ATGTATGCATGC
* *
44476 ATGTATGTATGT
1 ATGTATGCATGC
* *
44488 ATGTATGAAATGG
1 ATGTATG-CATGC
*
44501 ATGGATGCATGC
1 ATGTATGCATGC
44513 A
1 A
44514 GAGCTGGACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
12 33 0.79
13 9 0.21
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (12 bp):
ATGTATGCATGC
Found at i:44531 original size:15 final size:15
Alignment explanation
Indices: 44511--44544 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
44501 ATGGATGCAT
*
44511 GCAGAGCTGGACTTC
1 GCAGAGCTGGACTTA
44526 GCAGAGCTGGACTTA
1 GCAGAGCTGGACTTA
44541 GCAG
1 GCAG
44545 GGCAGGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (15 bp):
GCAGAGCTGGACTTA
Found at i:52655 original size:49 final size:47
Alignment explanation
Indices: 52534--52676 Score: 189
Period size: 48 Copynumber: 3.0 Consensus size: 47
52524 GTGCATAGAA
* * * *
52534 GGTGTG-AAAAAGCTGAGTTAGTGTTAAATTAGGAAAAGTGTGACTTC
1 GGTGTGAAAAAAGATGACTTAGTGTTGAATT-GGGAAAGTGTGACTTC
*
52581 TGTGTGAAAAAAGATGACTTAGTGTTGAATTGGGAAACGTGTGACTTC
1 GGTGTGAAAAAAGATGACTTAGTGTTGAATTGGGAAA-GTGTGACTTC
* *
52629 GGTGTATAAAAAAGATGACTTAGTGTTGAATTGGGAAAGTTTGACTTC
1 GGTGT-GAAAAAAGATGACTTAGTGTTGAATTGGGAAAGTGTGACTTC
52677 TTGGTGACTA
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
47 10 0.12
48 44 0.52
49 31 0.36
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (47 bp):
GGTGTGAAAAAAGATGACTTAGTGTTGAATTGGGAAAGTGTGACTTC
Found at i:57198 original size:24 final size:25
Alignment explanation
Indices: 57148--57201 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
57138 AATGAAAGGC
*
57148 TGAATTTAATGGATATTTTGAACAG
1 TGAATTTAATGGACATTTTGAACAG
*
57173 TGAATTTAAT-GACATTTTGAATAG
1 TGAATTTAATGGACATTTTGAACAG
57197 TGAAT
1 TGAAT
57202 AAATGTTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (25 bp):
TGAATTTAATGGACATTTTGAACAG
Found at i:59879 original size:178 final size:174
Alignment explanation
Indices: 59580--60053 Score: 469
Period size: 178 Copynumber: 2.7 Consensus size: 174
59570 GGAGGTTGTC
* * * * *
59580 GATCTCCAAATATTATAATTTTTTTTGAATGTCCCACAGTGGATTTAGTTTCAATAT-AGAAA-A
1 GATCTCCAAAAATTCTAA-TTTTTTTGAAAGTCCCTCAGTGGATGTAGTTTCAATATGA-AAATA
* * * * * * *
59643 TTCAGCACAAAATTCCTTATGTACAATTCTCTGGAAATCCATCAATTACAAGTCCCAAAAT-TTC
64 TTTAGCACAAAATTCCTTCTGTAAAATTCTCT-GAAATTCGTCAATCACAAGTCCCAAAATATGC
* * *
59707 TAATCAAACATAAGATCAACTTCA-ACAATGTTTTTAAGGGGGTTTTTT
128 CAATCAAACATAAGATCAACTTCAGA-AATATTTTTAAGGGGG-TTTAT
** * *
59755 GATCTCCAAAAATTCTAAATTGTTTTTGAAAGTCCCTCAGTGGGCGTAGTCTAAATATGGAAAAT
1 GATCTCCAAAAATTCT-AATT-TTTTTGAAAGTCCCTCAGTGGATGTAGTTTCAATAT-GAAAAT
* * * *
59820 ATTTAGCACAAAATTTCTTCTTTAGAATTCTCTAGAAATTTGTCAATCACAAGTCCC-AAATATG
63 ATTTAGCACAAAATTCCTTCTGTAAAATTCTCT-GAAATTCGTCAATCACAAGTCCCAAAATATG
* * * * *
59884 CCGATCAAACATATGATCAACTTGAGAATTATTTTTGAGGGGGTTTAT
127 CCAATCAAACATAAGATCAACTTCAGAAATATTTTTAAGGGGGTTTAT
* * * *
59932 GATCTCCAAAGATTCTGATTTTTTTTAATA-TCCCTCAATGGATGTAGTTTCAATATGAAAAT-T
1 GATCTCCAAAAATTCTAATTTTTTTGAA-AGTCCCTCAGTGGATGTAGTTTCAATATGAAAATAT
* *
59995 TTCAACACAAAATTCCTTCCGTAAAATTCTCTGAAAATTCGTCAA-CGACAAGTCCCAAA
65 TT-AGCACAAAATTCCTTCTGTAAAATTCTCTG-AAATTCGTCAATC-ACAAGTCCCAAA
60054 TCTATCGATC
Statistics
Matches: 245, Mismatches: 42, Indels: 24
0.79 0.14 0.08
Matches are distributed among these distances:
173 5 0.02
174 49 0.20
175 46 0.19
176 35 0.14
177 26 0.11
178 83 0.34
179 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (174 bp):
GATCTCCAAAAATTCTAATTTTTTTGAAAGTCCCTCAGTGGATGTAGTTTCAATATGAAAATATT
TAGCACAAAATTCCTTCTGTAAAATTCTCTGAAATTCGTCAATCACAAGTCCCAAAATATGCCAA
TCAAACATAAGATCAACTTCAGAAATATTTTTAAGGGGGTTTAT
Found at i:60244 original size:16 final size:17
Alignment explanation
Indices: 60198--60244 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
60188 TTGTGGATTT
*
60198 TTTTTTACTTTTTTGGCG
1 TTTTTTA-TTTTTTGGCA
*
60216 TTTTATATTTTTT-GCA
1 TTTTTTATTTTTTGGCA
60232 TTTTTTATTTTTT
1 TTTTTTATTTTTT
60245 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 6 0.23
18 6 0.23
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTTTATTTTTTGGCA
Found at i:60256 original size:17 final size:18
Alignment explanation
Indices: 60216--60254 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
60206 TTTTTTGGCG
60216 TTTTATATTTTTTGCATT
1 TTTTATATTTTTTGCATT
* *
60234 TTTTATTTTTTTTTCATT
1 TTTTATATTTTTTGCATT
60252 TTT
1 TTT
60255 ATGAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATATTTTTTGCATT
Found at i:60400 original size:16 final size:16
Alignment explanation
Indices: 60379--60412 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
60369 TAATTTCACC
60379 TTATGCATGTACCACT
1 TTATGCATGTACCACT
60395 TTATGCATGTACCACT
1 TTATGCATGTACCACT
60411 TT
1 TT
60413 CTCAATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (16 bp):
TTATGCATGTACCACT
Found at i:70423 original size:45 final size:46
Alignment explanation
Indices: 70359--70541 Score: 291
Period size: 46 Copynumber: 4.0 Consensus size: 46
70349 GTAACCATGC
* * *
70359 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTTAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
70404 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
* **
70450 AAATAAGCTTACGAGATTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
70496 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTACATT-GTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
70540 AA
1 AA
70542 TATTGGATAT
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
44 5 0.04
45 39 0.30
46 84 0.66
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
Found at i:71626 original size:22 final size:22
Alignment explanation
Indices: 71601--71667 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
71591 CAAAAATGCA
71601 AATGGGTACCGATACCCCTATG
1 AATGGGTACCGATACCCCTATG
* *
71623 AATGGGTATCAATACCCCCTATG
1 AATGGGTACCGATA-CCCCTATG
* *
71646 AATGTGTACCGATACCCTTATG
1 AATGGGTACCGATACCCCTATG
71668 GTATCAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 19 0.50
23 19 0.50
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (22 bp):
AATGGGTACCGATACCCCTATG
Found at i:71692 original size:32 final size:32
Alignment explanation
Indices: 71651--71771 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 32
71641 CTATGAATGT
71651 GTACCGATACCCTTATGGTATCAATACCTTGG
1 GTACCGATACCCTTATGGTATCAATACCTTGG
71683 GTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATG
1 GTACCGATA-CCCT-T-A-T-GGTATCAATA---CCT-TG---G
* *
71727 TGTACCGATTCCCCTATGGTATCAATACCTTGG
1 -GTACCGATACCCTTATGGTATCAATACCTTGG
71760 GTACCGATACCC
1 GTACCGATACCC
71772 CTCTGACTGG
Statistics
Matches: 73, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
32 20 0.27
33 5 0.07
34 1 0.01
35 1 0.01
36 3 0.04
37 13 0.18
40 13 0.18
41 3 0.04
42 1 0.01
43 1 0.01
44 4 0.05
45 8 0.11
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (32 bp):
GTACCGATACCCTTATGGTATCAATACCTTGG
Found at i:71715 original size:37 final size:37
Alignment explanation
Indices: 71667--71792 Score: 136
Period size: 37 Copynumber: 3.3 Consensus size: 37
71657 ATACCCTTAT
71667 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
1 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
*
71704 GGTATCAATACCCCCTATGAATGTGTACCGAT-TCCC-CT-A-T-
1 GGTATCAATA---CCT-TG---G-GTACCGATACCCCTCTGACTG
71744 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
1 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
71781 GGTATCAATACC
1 GGTATCAATACC
71793 CCAATAAAGG
Statistics
Matches: 74, Mismatches: 2, Indels: 26
0.73 0.02 0.25
Matches are distributed among these distances:
32 8 0.11
33 4 0.05
34 2 0.03
35 1 0.01
36 3 0.04
37 25 0.34
40 13 0.18
41 3 0.04
42 1 0.01
43 2 0.03
44 4 0.05
45 8 0.11
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (37 bp):
GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
Found at i:71730 original size:77 final size:77
Alignment explanation
Indices: 71603--71794 Score: 348
Period size: 77 Copynumber: 2.5 Consensus size: 77
71593 AAAATGCAAA
* * *
71603 TGGGTACCGATACCCCTATGAATGGGTATCAATACCCCCTATGAATGTGTACCGATACCCTTATG
1 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATACCCCTATG
71668 GTATCAATACCT
66 GTATCAATACCT
*
71680 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATTCCCCTATG
1 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATACCCCTATG
71745 GTATCAATACCT
66 GTATCAATACCT
71757 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCC
1 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCC
71795 AATAAAGGCT
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 111 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (77 bp):
TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATACCCCTATG
GTATCAATACCT
Found at i:71868 original size:33 final size:33
Alignment explanation
Indices: 71823--71888 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
71813 GAATGAAAAA
*
71823 AGGTACCGATACCC-CTATAGGTATCAATACCCT
1 AGGTACCAATACCCTC-ATAGGTATCAATACCCT
*
71856 AGGTACCAATACCCTGCATGGGTATCAATACCC
1 AGGTACCAATACCCT-CATAGGTATCAATACCC
71889 CTAGCTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.45
34 15 0.52
35 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (33 bp):
AGGTACCAATACCCTCATAGGTATCAATACCCT
Found at i:71888 original size:19 final size:15
Alignment explanation
Indices: 71840--71870 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71830 GATACCCCTA
71840 TAGGTATCAATACCC
1 TAGGTATCAATACCC
*
71855 TAGGTACCAATACCC
1 TAGGTATCAATACCC
71870 T
1 T
71871 GCATGGGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (15 bp):
TAGGTATCAATACCC
Found at i:73782 original size:17 final size:17
Alignment explanation
Indices: 73757--73798 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
73747 ATTATGGTTA
73757 AAATAAAAAATAAGAATT
1 AAAT-AAAAATAAGAATT
*
73775 AAATAAAAATAATAATT
1 AAATAAAAATAAGAATT
73792 AAATAAA
1 AAATAAA
73799 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATAAAAATAAGAATT
Found at i:75009 original size:11 final size:11
Alignment explanation
Indices: 74993--75033 Score: 73
Period size: 11 Copynumber: 3.6 Consensus size: 11
74983 CTTTCAGTTG
74993 ATTATTATTTT
1 ATTATTATTTT
75004 ATTATTATTTT
1 ATTATTATTTT
75015 ATTATTATTATT
1 ATTATTATT-TT
75027 ATTATTA
1 ATTATTA
75034 ATAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:75012 original size:14 final size:15
Alignment explanation
Indices: 74993--75033 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
74983 CTTTCAGTTG
74993 ATTATTATT-TTATT
1 ATTATTATTATTATT
75007 ATTATT-TTATTATT
1 ATTATTATTATTATT
75021 ATTATTATTATTA
1 ATTATTATTATTA
75034 ATAAAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 2 0.08
14 17 0.68
15 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTATTATTATTATT
Found at i:75046 original size:3 final size:3
Alignment explanation
Indices: 74993--75033 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
74983 CTTTCAGTTG
74993 ATT ATT ATT -TT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
75034 ATAAAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:76293 original size:14 final size:14
Alignment explanation
Indices: 76274--76303 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
76264 TTTAATTTCT
76274 TTATATTTTAGTTA
1 TTATATTTTAGTTA
76288 TTATATTTTAGTTA
1 TTATATTTTAGTTA
76302 TT
1 TT
76304 TGCAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTATATTTTAGTTA
Done.