Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008153.1 Hibiscus syriacus cultivar Beakdansim tig00110719_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: 58423
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2746 original size:20 final size:20
Alignment explanation
Indices: 2717--2768 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2707 AGCTCTTTGC
*
2717 GGTGAGTCACCAAACTATGT
1 GGTGACTCACCAAACTATGT
2737 GGTGACTCACCAAACTATGT
1 GGTGACTCACCAAACTATGT
2757 GGTGACTCACCA
1 GGTGACTCACCA
2769 TAAGGCATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
GGTGACTCACCAAACTATGT
Found at i:3395 original size:17 final size:17
Alignment explanation
Indices: 3373--3433 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
3363 GTTGAACAAA
3373 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
* *
3390 TTCTTCTTCTTTCA-GATGAG
1 TTCTTC-TCATT-ATGA--AC
3410 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
3427 TCCTTCT
1 TTCTTCT
3434 GGAAATGCCG
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 13 0.38
18 7 0.21
19 7 0.21
20 7 0.21
ACGTcount: A:0.18, C:0.25, G:0.08, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:3626 original size:117 final size:111
Alignment explanation
Indices: 3495--3869 Score: 377
Period size: 113 Copynumber: 3.3 Consensus size: 111
3485 GAATTAAGGC
* *
3495 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTGTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCTCATTAT
* *
3560 GAACACT-TCTGGAAATGTTGATGCTATCTATCTTCTGTGAT-AGAGTCATG-AA
66 GAACACTCTCTGGAAA-GTTGAT-C---C-ATC--CAGTGATGA-AGTCAAGCAA
* *
3612 AAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTTTTCC-TCTTCAGATAAGTTCTTCT--TTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TTCTCCTTCTTCAGATAAGTTCTTCTCATTA
** * *
3674 TGAACTTTCTCTGGAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
65 TGAACACTCTCTGGAAAGTTGATCCATCCAGTGATGAAGTCAAGCAA
* * *
3721 AAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATAAGTTCTTCTCATTA
** * * * * * *
3786 TGAACTTTATCTAGCAATGCTGATCCATCAAGTGATGAATTCAAGCAA
65 TGAACACTCTCT-GGAAAGTTGATCCATCCAGTGATGAAGTCAAGCAA
* * *
3834 AATGTTGAACAAATTCTTCTCA-TATGAATTTCTTCT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
3870 TCATGATGAA
Statistics
Matches: 227, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
108 12 0.05
109 35 0.15
110 22 0.10
111 2 0.01
112 27 0.12
113 51 0.22
114 1 0.00
115 15 0.07
116 8 0.04
117 49 0.22
118 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (111 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATAAGTTCTTCTCATTAT
GAACACTCTCTGGAAAGTTGATCCATCCAGTGATGAAGTCAAGCAA
Found at i:3842 original size:113 final size:110
Alignment explanation
Indices: 3480--3871 Score: 399
Period size: 117 Copynumber: 3.5 Consensus size: 110
3470 TGGTTCATAT
* *
3480 GTGATGAATT-AAGGC-AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAG
1 GTGATGAATTCAA-GCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * ** **
3542 ATGAGTTGTTCTCATTATGAACACTTCTGGAAATGTTGATGCTATCTATCTTCT
65 ATAAGTTCTTCTCATTATGAACTTTTCT-GAAATGTTGAT-C---C-ATC--AA
* * * * *
3596 GTGAT-AGAGTCATG-AAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTTTTCC-TCTTCA
1 GTGATGA-ATTCAAGCAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
3658 GATAAGTTCTTCT--TTATGAACTTTCTCTGGAAA-GTTGATCCATCGA
64 GATAAGTTCTTCTCATTATGAACTTT-TCT-GAAATGTTGATCCATCAA
*
3704 GTGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAAGCAAAAG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
3769 ATAAGTTCTTCTCATTATGAACTTTATCTAGCAATGCTGATCCATCAA
65 ATAAGTTCTTCTCATTATGAACTTT-TCT-GAAATGTTGATCCATCAA
*
3817 GTGATGAATTCAAGCAAAATGTTGAACAAATTCTTCTCA-TATGAATTTCTTCTTC
1 GTGATGAATTCAAGCAAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
3872 ATGATGAATT
Statistics
Matches: 240, Mismatches: 22, Indels: 32
0.82 0.07 0.11
Matches are distributed among these distances:
108 11 0.05
109 37 0.15
110 22 0.09
111 1 0.00
112 33 0.14
113 48 0.20
114 2 0.01
115 16 0.07
116 18 0.08
117 49 0.20
118 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (110 bp):
GTGATGAATTCAAGCAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TAAGTTCTTCTCATTATGAACTTTTCTGAAATGTTGATCCATCAA
Found at i:3880 original size:18 final size:17
Alignment explanation
Indices: 3847--3889 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
3837 GTTGAACAAA
3847 TTCTTC-TCATATGAAT
1 TTCTTCTTCATATGAAT
3863 TTCTTCTTCATGATGAAT
1 TTCTTCTTCAT-ATGAAT
3881 TTCTTCTTC
1 TTCTTCTTC
3890 CTTCTTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 15 0.60
ACGTcount: A:0.19, C:0.21, G:0.07, T:0.53
Consensus pattern (17 bp):
TTCTTCTTCATATGAAT
Found at i:3887 original size:130 final size:133
Alignment explanation
Indices: 3734--4003 Score: 415
Period size: 130 Copynumber: 2.1 Consensus size: 133
3724 ATTGAACAAA
* * *
3734 TTCTTC-TCATTATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTATCT
1 TTCTTCTTCATGATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCT
** *
3798 AGCAATGCTGATCCATCAAGTGATGAATTCAAGCAAAATGTTGAACAA-ATTCTTCTCA-TATGA
66 AGCAATGCCAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGATTCTTCTCATTATGA
3861 A-T
131 ACT
*
3863 TTCTTCTTCATGATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT
1 TTCTTCTTCATGATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCT
* * *
3928 GGCAATGCCAATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAGTTTCTTCTCATTATGA
66 AGCAATGCCAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGATTCTTCTCATTATGA
3993 ACT
131 ACT
3996 TT-TTCTTC
1 TTCTTCTTC
4004 CTCTTCAGAT
Statistics
Matches: 127, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
129 6 0.05
130 97 0.76
131 9 0.07
132 12 0.09
133 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (133 bp):
TTCTTCTTCATGATGAATTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTCTACCT
AGCAATGCCAATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGATTCTTCTCATTATGA
ACT
Found at i:4451 original size:22 final size:22
Alignment explanation
Indices: 4426--4575 Score: 141
Period size: 22 Copynumber: 7.1 Consensus size: 22
4416 AAATCCAATA
* *
4426 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
*
4448 AATCTATAATCTTTG--AAGAG
1 AATCTATCATCTTTGAAAAGAG
** *
4468 AAAATATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
* *
4490 TATCTATCATATTTG--AAGAG
1 AATCTATCATCTTTGAAAAGAG
4510 AATCTATCATCTTTGAAAAGA-
1 AATCTATCATCTTTGAAAAGAG
* * *
4531 AA-ATATCATATTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
* *
4552 AATTTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
4574 AA
1 AA
4576 GATGTAGATA
Statistics
Matches: 103, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
20 49 0.48
21 4 0.04
22 50 0.49
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:4468 original size:20 final size:20
Alignment explanation
Indices: 4443--4572 Score: 143
Period size: 20 Copynumber: 6.3 Consensus size: 20
4433 CTTCTTTGAA
*
4443 AAGAGAATCTATAATCTTTG
1 AAGAGAATCTATCATCTTTG
**
4463 AAGAGAAAATATCATCTTTG
1 AAGAGAATCTATCATCTTTG
*
4483 AAGAGAGTATCTATCATATTTG
1 AAGAGA--ATCTATCATCTTTG
4505 AAGAGAATCTATCATCTTTG
1 AAGAGAATCTATCATCTTTG
* ** *
4525 AAAAGAAAATATCATATTTG
1 AAGAGAATCTATCATCTTTG
*
4545 AAGAGAGAATTTATCATCTTTG
1 -A-AGAGAATCTATCATCTTTG
4567 AAGAGA
1 AAGAGA
4573 GAAGATGTAG
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
20 57 0.63
21 2 0.02
22 32 0.35
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.32
Consensus pattern (20 bp):
AAGAGAATCTATCATCTTTG
Found at i:4495 original size:42 final size:42
Alignment explanation
Indices: 4435--4575 Score: 169
Period size: 42 Copynumber: 3.4 Consensus size: 42
4425 AAATCTTTCT
* * *
4435 TCTTTGAAAAGAGAATCTATAATCTTTGAAGAGAAAATATCA
1 TCTTTGAAGAGAGAATCTATCATATTTGAAGAGAAAATATCA
* **
4477 TCTTTGAAGAGAGTATCTATCATATTTGAAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCATATTTGAAGAGAAAATATCA
** *
4519 TCTTTGAA-A-AGAAAATATCATATTTGAAGAGAGAATTTATCA
1 TCTTTGAAGAGAGAATCTATCATATTTGAAGAGA-AA-ATATCA
4561 TCTTTGAAGAGAGAA
1 TCTTTGAAGAGAGAA
4576 GATGTAGATA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 20 0.24
41 2 0.02
42 57 0.68
43 1 0.01
44 4 0.05
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (42 bp):
TCTTTGAAGAGAGAATCTATCATATTTGAAGAGAAAATATCA
Found at i:4545 original size:62 final size:62
Alignment explanation
Indices: 4443--4572 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 62
4433 CTTCTTTGAA
* * *
4443 AAGAGAATCTATAATCTTTGAAGAGAAAATATCATCTTTGAAGAGAGTATCTATCATATTTG
1 AAGAGAATCTATAATCTTTGAAAAGAAAATATCATATTTGAAGAGAGAATCTATCATATTTG
* * *
4505 AAGAGAATCTATCATCTTTGAAAAGAAAATATCATATTTGAAGAGAGAATTTATCATCTTTG
1 AAGAGAATCTATAATCTTTGAAAAGAAAATATCATATTTGAAGAGAGAATCTATCATATTTG
4567 AAGAGA
1 AAGAGA
4573 GAAGATGTAG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.32
Consensus pattern (62 bp):
AAGAGAATCTATAATCTTTGAAAAGAAAATATCATATTTGAAGAGAGAATCTATCATATTTG
Found at i:5993 original size:75 final size:74
Alignment explanation
Indices: 5824--6044 Score: 268
Period size: 74 Copynumber: 3.0 Consensus size: 74
5814 ATGTCCTAAC
* * * * *
5824 ATTTGCTGATACAGACGTTCAAAATGCACCAACATTCGTGATTCTGATT-AAAAGGGCTTTCAGT
1 ATTTGCTGATACAAACGTTCAAAATGCATCAATATTC-TGATTCTGATTGAAATGGGCTTTCAGC
5888 ATGCCCCAGT
65 ATGCCCCAGT
*
5898 ATTTGCTGATACAAATGTTCAAAATG-AGTCAATATTCTTGATTCTGATTGAAATGGGCTTTCAG
1 ATTTGCTGATACAAACGTTCAAAATGCA-TCAATATTC-TGATTCTGATTGAAATGGGCTTTCAG
*
5962 CCTGCCCCAGT
64 CATGCCCCAGT
* * ** * *
5973 ATTTGCTGATAGAAACGTTC-AAATGCATTAATATTCCAACTTCTAATTGAAATGGGCTTTCAAC
1 ATTTGCTGATACAAACGTTCAAAATGCATCAATATTCTGA-TTCTGATTGAAATGGGCTTTCAGC
6037 ATGCCCCA
65 ATGCCCCA
6045 AATATTCATT
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
73 2 0.02
74 84 0.66
75 41 0.32
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (74 bp):
ATTTGCTGATACAAACGTTCAAAATGCATCAATATTCTGATTCTGATTGAAATGGGCTTTCAGCA
TGCCCCAGT
Found at i:9361 original size:21 final size:22
Alignment explanation
Indices: 9337--9378 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9327 TTGATTCAAA
9337 ATTTTTCT-TCTTTTCTTTTTC
1 ATTTTTCTCTCTTTTCTTTTTC
*
9358 ATTTTTCTCTTTTTTCTTTTT
1 ATTTTTCTCTCTTTTCTTTTT
9379 TTCGATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
ATTTTTCTCTCTTTTCTTTTTC
Found at i:9378 original size:7 final size:7
Alignment explanation
Indices: 9338--9379 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
9328 TGATTCAAAA
9338 TTTTTCT
1 TTTTTCT
9345 TCTTTTC-
1 T-TTTTCT
9352 TTTTTCAT
1 TTTTTC-T
9360 TTTTCTCT
1 TTTT-TCT
9368 TTTTTCT
1 TTTTTCT
9375 TTTTT
1 TTTTT
9380 TCGATGAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.16
7 10 0.32
8 14 0.45
9 2 0.06
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:12528 original size:14 final size:15
Alignment explanation
Indices: 12511--12547 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12501 CAAAGATGCA
12511 AATGCAAATAA-AAC
1 AATGCAAATAATAAC
*
12525 AATGCAAA-AATAAG
1 AATGCAAATAATAAC
12539 AATGCAAAT
1 AATGCAAAT
12548 TGTGCAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (15 bp):
AATGCAAATAATAAC
Found at i:12581 original size:7 final size:7
Alignment explanation
Indices: 12571--12611 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
12561 AGCAAACAAC
12571 AAATGCA
1 AAATGCA
12578 AAATG-A
1 AAATGCA
12584 AAATGCA
1 AAATGCA
*
12591 AAGATGTA
1 AA-ATGCA
12599 AAATGC-
1 AAATGCA
12605 AAATGCA
1 AAATGCA
12612 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 12 0.41
7 11 0.38
8 6 0.21
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (7 bp):
AAATGCA
Found at i:16302 original size:3 final size:3
Alignment explanation
Indices: 16296--16376 Score: 116
Period size: 3 Copynumber: 28.0 Consensus size: 3
16286 CCTGTTTGTT
16296 ATA ATA ATA ATA AT- ATA ATA ATA ATTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
*
16341 AT- ATA A-A ATA ATA ATA ATA ATA GTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16377 TTATTAAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
2 8 0.11
3 60 0.85
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16393 original size:25 final size:24
Alignment explanation
Indices: 16298--16393 Score: 92
Period size: 25 Copynumber: 4.1 Consensus size: 24
16288 TGTTTGTTAT
**
16298 AATAATAATAATATAATAATAATT
1 AATAATAATAATATAATAATAAAA
*
16322 AATAATAATAATAATAATAATATAA
1 AATAATAATAAT-ATAATAATAAAA
*
16347 AATAATAAT-A-ATAATAGT--AA
1 AATAATAATAATATAATAATAAAA
* *
16367 AATAATAATATTATTAAAAATAAAA
1 AATAATAATAATA-TAATAATAAAA
16392 AA
1 AA
16394 CAAATGGATA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
20 11 0.19
22 8 0.14
23 5 0.08
24 13 0.22
25 22 0.37
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (24 bp):
AATAATAATAATATAATAATAAAA
Found at i:16997 original size:21 final size:20
Alignment explanation
Indices: 16936--17073 Score: 96
Period size: 21 Copynumber: 6.8 Consensus size: 20
16926 ATTTTTGTGC
16936 ATAGAGTATCGATA-CCCTTA
1 ATAG-GTATCGATACCCCTTA
*
16956 TACAGGTATCGATACCCCCTTGA
1 -ATAGGTATCGATA-CCCCTT-A
16979 ATAGGTATCGATACCCCTTGA
1 ATAGGTATCGATACCCCTT-A
*
17000 ATAGGTATCGAT---CTTTGA
1 ATAGGTATCGATACCCCTT-A
17018 AT-GAGTATCGATACCCCCCTT-
1 ATAG-GTATCGATA--CCCCTTA
*
17039 AT-GGTATCAATACCCCCTT-
1 ATAGGTATCGATA-CCCCTTA
17058 AT-GGTATCGATACCCC
1 ATAGGTATCGATACCCC
17074 CTGTCAGGTT
Statistics
Matches: 102, Mismatches: 6, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
17 1 0.01
18 19 0.19
19 18 0.18
20 17 0.17
21 26 0.25
22 17 0.17
23 4 0.04
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (20 bp):
ATAGGTATCGATACCCCTTA
Found at i:17056 original size:19 final size:19
Alignment explanation
Indices: 17022--17075 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
17012 CTTTGAATGA
17022 GTATCGATACCCCCCTTATG
1 GTATCGATA-CCCCCTTATG
*
17042 GTATCAATACCCCCTTATG
1 GTATCGATACCCCCTTATG
17061 GTATCGATACCCCCT
1 GTATCGATACCCCCT
17076 GTCAGGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACCCCCTTATG
Found at i:19661 original size:22 final size:19
Alignment explanation
Indices: 19607--19741 Score: 105
Period size: 18 Copynumber: 6.8 Consensus size: 19
19597 GAATGCTCGG
*
19607 ATGGTACCGATACCTCCAT
1 ATGGTACCGATACCCCCAT
* *
19626 A-GGTATCGACACCCCCAT
1 ATGGTACCGATACCCCCAT
19644 GCAATGGTACCGATACCCCCAT
1 ---ATGGTACCGATACCCCCAT
* *
19666 A-GGTATCGACACCCCCAT
1 ATGGTACCGATACCCCCAT
19684 GCAATGGTACCGATACCCCCAT
1 ---ATGGTACCGATACCCCCAT
* *
19706 A-GGTATCGATACCCCTAT
1 ATGGTACCGATACCCCCAT
19724 GCAATGGTACCGATACCC
1 ---ATGGTACCGATACCC
19742 TCAGGCATAT
Statistics
Matches: 92, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
18 44 0.48
19 3 0.03
21 3 0.03
22 42 0.46
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (19 bp):
ATGGTACCGATACCCCCAT
Found at i:19666 original size:40 final size:40
Alignment explanation
Indices: 19607--19741 Score: 243
Period size: 40 Copynumber: 3.4 Consensus size: 40
19597 GAATGCTCGG
*
19607 ATGGTACCGATACCTCCATAGGTATCGACACCCCCATGCA
1 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA
19647 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA
1 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA
* *
19687 ATGGTACCGATACCCCCATAGGTATCGATACCCCTATGCA
1 ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA
19727 ATGGTACCGATACCC
1 ATGGTACCGATACCC
19742 TCAGGCATAT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 92 1.00
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (40 bp):
ATGGTACCGATACCCCCATAGGTATCGACACCCCCATGCA
Found at i:23914 original size:59 final size:60
Alignment explanation
Indices: 23788--23920 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
23778 ATATTTGAAC
** * *
23788 TTCATCCTTAAACTATGACTATCATTCTAAATTAGTCCTCAAAATTTTGAACATTTCAAT
1 TTCATCCCCAAACTATGACTATCATTCAAAATTAGTCCTCAAAATTTTGAACATTCCAAT
* * * *
23848 TTCATCCCCAAACTATGACCT-TTATTCAAAATTGGTCC-CAAACTTTTTAACATTCCAAT
1 TTCATCCCCAAACTATGA-CTATCATTCAAAATTAGTCCTCAAAATTTTGAACATTCCAAT
23907 TTCAT-CCCAAACTA
1 TTCATCCCCAAACTA
23921 AATATATATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 9 0.14
59 23 0.36
60 30 0.47
61 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (60 bp):
TTCATCCCCAAACTATGACTATCATTCAAAATTAGTCCTCAAAATTTTGAACATTCCAAT
Found at i:40511 original size:19 final size:19
Alignment explanation
Indices: 40489--40525 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40479 CCAGAATAAT
*
40489 GACCGGTAGCGTGAATAGC
1 GACCGGTAGCATGAATAGC
*
40508 GACCGGTGGCATGAATAG
1 GACCGGTAGCATGAATAG
40526 TAACTGATCG
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:0.27, C:0.19, G:0.38, T:0.16
Consensus pattern (19 bp):
GACCGGTAGCATGAATAGC
Found at i:41161 original size:19 final size:18
Alignment explanation
Indices: 41111--41162 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
41101 TAGTACTTAA
41111 AATAAAATAAT-ATAATG
1 AATAAAATAATAATAATG
41128 AATAGAAAAACTAATAATAATG
1 AAT---AAAA-TAATAATAATG
41150 ACATAAAATAATA
1 A-ATAAAATAATA
41163 CCATTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.10
19 5 0.17
20 8 0.28
21 4 0.14
22 7 0.24
23 2 0.07
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (18 bp):
AATAAAATAATAATAATG
Found at i:42997 original size:14 final size:16
Alignment explanation
Indices: 42980--43012 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42970 CATACATGCA
42980 TTTGCA-TTCT-CATT
1 TTTGCATTTCTGCATT
42994 TTTGCATTTCTGCATT
1 TTTGCATTTCTGCATT
43010 TTT
1 TTT
43013 TATATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.12, C:0.18, G:0.09, T:0.61
Consensus pattern (16 bp):
TTTGCATTTCTGCATT
Found at i:43055 original size:20 final size:20
Alignment explanation
Indices: 43032--43162 Score: 72
Period size: 20 Copynumber: 6.5 Consensus size: 20
43022 TTTACATTCA
43032 CATCTTTGCATTTGCATTTG
1 CATCTTTGCATTTGCATTTG
* * * *
43052 CATCTTTACGTTTGTATTTA
1 CATCTTTGCATTTGCATTTG
* **
43072 CAT-TTT-CATTTTACATTCA
1 CATCTTTGCA-TTTGCATTTG
*
43091 CATCTTTGCATTTGCATTCG
1 CATCTTTGCATTTGCATTTG
* * * *
43111 TATCTTTACGTTTGTATTT-
1 CATCTTTGCATTTGCATTTG
* *
43130 -ATATTTTCATTTTTTGCATTTG
1 CATCTTTGCA---TTTGCATTTG
43152 CATCTTTGCAT
1 CATCTTTGCAT
43163 AGTTATATTT
Statistics
Matches: 82, Mismatches: 21, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
18 7 0.09
19 13 0.16
20 45 0.55
21 10 0.12
23 7 0.09
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (20 bp):
CATCTTTGCATTTGCATTTG
Found at i:43070 original size:26 final size:25
Alignment explanation
Indices: 43036--43085 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
43026 CATTCACATC
*
43036 TTTGCATTTGCATTTGCATCTTTACG
1 TTTGCATTTACATTTGCAT-TTTACG
* *
43062 TTTGTATTTACATTTTCATTTTAC
1 TTTGCATTTACATTTGCATTTTAC
43086 ATTCACATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (25 bp):
TTTGCATTTACATTTGCATTTTACG
Found at i:43088 original size:59 final size:59
Alignment explanation
Indices: 43017--43142 Score: 225
Period size: 59 Copynumber: 2.1 Consensus size: 59
43007 ATTTTTTATA
*
43017 TTCATTTTACATTCACATCTTTGCATTTGCATTTGCATCTTTACGTTTGTATTTACATT
1 TTCATTTTACATTCACATCTTTGCATTTGCATTCGCATCTTTACGTTTGTATTTACATT
* *
43076 TTCATTTTACATTCACATCTTTGCATTTGCATTCGTATCTTTACGTTTGTATTTATATT
1 TTCATTTTACATTCACATCTTTGCATTTGCATTCGCATCTTTACGTTTGTATTTACATT
43135 TTCATTTT
1 TTCATTTT
43143 TTGCATTTGC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (59 bp):
TTCATTTTACATTCACATCTTTGCATTTGCATTCGCATCTTTACGTTTGTATTTACATT
Found at i:51129 original size:117 final size:117
Alignment explanation
Indices: 50911--51130 Score: 261
Period size: 117 Copynumber: 1.9 Consensus size: 117
50901 TTTCAAATCG
* *
50911 AAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATTCTTCTTCAAGATTTCA
1 AAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTTCA
* * *
50976 TTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTGA
66 TTTTGATTTTCAAAATACATTTACGTTTCTAAAAGAAGTTTGTTTAATTTGA
* * * *
51028 AAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGACAA-CTCTAACTCCTT-TCTCAAAATT
1 AAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGA-AAGCTCTAAATCCTTCT-TCAAAATT
* *
51090 TCATTTTGATTTTCTAAATATAGTTTGAC-TTTC-AAAAGAAG
63 TCATTTTGATTTTCAAAATACA-TTT-ACGTTTCTAAAAGAAG
51131 ATTATTTTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
116 2 0.02
117 75 0.86
118 9 0.10
119 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (117 bp):
AAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTTCA
TTTTGATTTTCAAAATACATTTACGTTTCTAAAAGAAGTTTGTTTAATTTGA
Found at i:55886 original size:60 final size:61
Alignment explanation
Indices: 55719--55899 Score: 249
Period size: 62 Copynumber: 3.0 Consensus size: 61
55709 GAATCAATTT
*
55719 TTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCCGTAGAGTCAATCC
1 TTGACTT-CTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAGAGTCAATCC
* * * *
55781 TTGACTTTCTCTTGAAGAGAAGTCAACATTTATTATTTTTTACTCCTCAGTAGAGTCAATCC
1 TTGAC-TTCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAGAGTCAATCC
* * *
55843 TTGAC-TCTCGTGAAG-GAAAGTCAACCTTTATTATTCCTGACTCCCCAGTTGAGTCAA
1 TTGACTTCTCGTGAAGAG-AAGTCAACCTTTATTATTTCTGACTCCTCAGTAGAGTCAA
55900 ATTTTAACTT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 43 0.41
62 59 0.56
63 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (61 bp):
TTGACTTCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAGTAGAGTCAATCC
Found at i:56000 original size:36 final size:36
Alignment explanation
Indices: 55944--56428 Score: 749
Period size: 36 Copynumber: 13.5 Consensus size: 36
55934 TTATTCCTGA
* * *
55944 CTCCCCGGTAGAGTAGTGAAGCAAAGCCATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * *
55980 CTCCACGAAAGAGTGGTGAAGCAAAACAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
56016 CTCCATGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * *
56052 CTCCACGAAAAAGTAGTGAAGCAAAGCCATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
56088 CGCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * *
56124 CTCTACAGAAGAGTAGTGAAGCAAAGCAATCTTAAC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
* * **
56160 CTCCATGGAAGAGTAATGAAGTGAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
56196 CTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
56232 CTCCACGGAAGAGTAGTGAAGC-AAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
56267 CTCCACGGAAGAGTAGTGAATCAAAGCAATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
*
56303 CTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
56339 CTCCACGGAAGAGTAGTGAAGCAAAGTC-ATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAG-CAATCTTAGC
*
56375 CTCCACGGAAGAGTAGTGAAGCAAAGCTATCTTAGC
1 CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
56411 CTCCACGGAAGAGTAGTG
1 CTCCACGGAAGAGTAGTG
56429 GAACGAATTT
Statistics
Matches: 408, Mismatches: 38, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
35 34 0.08
36 373 0.91
37 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (36 bp):
CTCCACGGAAGAGTAGTGAAGCAAAGCAATCTTAGC
Done.