Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006438.1 Hibiscus syriacus cultivar Beakdansim tig00015548_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: 60155
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:482 original size:11 final size:11
Alignment explanation
Indices: 458--502 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
448 TTGGTGCTGG
458 AAACAAGATAA
1 AAACAAGATAA
* *
469 AAATAAGATTA
1 AAACAAGATAA
480 AAACAAGATAA
1 AAACAAGATAA
491 AGAA-AAGATAA
1 A-AACAAGATAA
502 A
1 A
503 TGATTGCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:486 original size:22 final size:22
Alignment explanation
Indices: 458--499 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
448 TTGGTGCTGG
458 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
480 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
500 AAATGATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:4767 original size:20 final size:20
Alignment explanation
Indices: 4744--4781 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4734 GCTTTTTTGT
4744 TTTTTTGTGTTTTTTTTGCC
1 TTTTTTGTGTTTTTTTTGCC
*
4764 TTTTTTGTTTTTTTTTTG
1 TTTTTTGTGTTTTTTTTG
4782 TAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (20 bp):
TTTTTTGTGTTTTTTTTGCC
Found at i:4779 original size:10 final size:9
Alignment explanation
Indices: 4736--4778 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
4726 AAATTTTGGC
4736 TTTTTTGTT
1 TTTTTTGTT
4745 TTTTTGTGTT
1 TTTTT-TGTT
**
4755 TTTTTTGCC
1 TTTTTTGTT
4764 TTTTTTGTT
1 TTTTTTGTT
4773 TTTTTT
1 TTTTTT
4779 TTGTAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.84
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:5124 original size:11 final size:11
Alignment explanation
Indices: 5100--5144 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
5090 TTGGTGCTGG
5100 AAACAAGATAA
1 AAACAAGATAA
* *
5111 AAATAAGATTA
1 AAACAAGATAA
5122 AAACAAGATAA
1 AAACAAGATAA
5133 AGAA-AAGATAA
1 A-AACAAGATAA
5144 A
1 A
5145 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:5128 original size:22 final size:22
Alignment explanation
Indices: 5100--5141 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5090 TTGGTGCTGG
5100 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
5122 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
5142 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:11564 original size:2 final size:2
Alignment explanation
Indices: 11559--11610 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
11549 ACACACACAG
11559 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
11601 AT AT AT AT AT
1 AT AT AT AT AT
11611 CTTTTTCCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14736 original size:23 final size:22
Alignment explanation
Indices: 14711--14801 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 22
14701 TGCCATATAT
* *
14711 TTGTCCCGAAGGACAACATAGTT
1 TTGTCCCGAAGGACCACATAG-A
* * *
14734 TTGTCTCGAATGATCACATAAGA
1 TTGTCCCGAAGGACCACAT-AGA
* *
14757 TTATCCTGAAGGACCACATAGGA
1 TTGTCCCGAAGGACCACATA-GA
*
14780 TTGTCCTGAAGGACCACATAGA
1 TTGTCCCGAAGGACCACATAGA
14802 ACCCTCAACT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
22 3 0.05
23 50 0.91
24 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (22 bp):
TTGTCCCGAAGGACCACATAGA
Found at i:16297 original size:19 final size:19
Alignment explanation
Indices: 16273--16323 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
16263 GAAAATATTC
16273 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
16292 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
16311 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
16324 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:16299 original size:65 final size:65
Alignment explanation
Indices: 16166--16325 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
16156 TGCACCAAGT
* * * ***
16166 GTGCATCGTTGCATGAAGTGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGA
* **
16230 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAG
16294 A
65 A
* *
16295 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
16326 CAATTAATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 34 0.41
65 48 0.59
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGAGA
Found at i:17007 original size:17 final size:17
Alignment explanation
Indices: 16985--17028 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
16975 AATAGTCAAG
*
16985 CATCCAAATATCATAAA
1 CATCCAAATAACATAAA
*
17002 CATCCAAACAAACATAAA
1 CATCCAAA-TAACATAAA
17020 CATCCAAAT
1 CATCCAAAT
17029 CAAAAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (17 bp):
CATCCAAATAACATAAA
Found at i:17019 original size:18 final size:19
Alignment explanation
Indices: 16996--17032 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
16986 ATCCAAATAT
16996 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
17014 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
17033 AAGTTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:24351 original size:55 final size:55
Alignment explanation
Indices: 24283--24394 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
24273 TCCTAATGTT
24283 GATATCTTTGCTTAACAAACAAGTGAACCGCTACCAGTCCCTTCAAGGGAAGACC
1 GATATCTTTGCTTAACAAACAAGTGAACCGCTACCAGTCCCTTCAAGGGAAGACC
24338 GATATCTTTGCTTAACAAACAAGTGAACCGCTACCAGTCCCTTCAAGGGAAGACC
1 GATATCTTTGCTTAACAAACAAGTGAACCGCTACCAGTCCCTTCAAGGGAAGACC
24393 GA
1 GA
24395 CGATCTCTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (55 bp):
GATATCTTTGCTTAACAAACAAGTGAACCGCTACCAGTCCCTTCAAGGGAAGACC
Found at i:26815 original size:24 final size:24
Alignment explanation
Indices: 26788--26887 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
26778 GATATCAAAA
*
26788 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
26812 ATCATAACAGAATCCAGTTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
26836 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
26860 GTTAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
26884 ATCA
1 ATCA
26888 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 52 0.93
25 2 0.04
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:26887 original size:48 final size:48
Alignment explanation
Indices: 26781--26889 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
26771 AAACGGAGAT
* * * * *
26781 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
26829 TTTAGGAATCAGAACAGATTTCAGATCAGATGTTAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
26877 ATCAGAAATCAGA
1 ATCAGAAATCAGA
26890 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:29419 original size:19 final size:19
Alignment explanation
Indices: 29397--29479 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
29387 CTAGGCGGCT
*
29397 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
29416 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
29435 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
29449 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
29468 CGGCTCGGCTCA
1 CGGCTCGGCTCA
29480 AATGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:29426 original size:14 final size:14
Alignment explanation
Indices: 29421--29460 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
29411 TCAAACGGCT
*
29421 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
29435 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
29449 CGGCTCGGCTCA
1 CGGCTCGGCTCA
29461 GCTCAAGCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:29450 original size:33 final size:33
Alignment explanation
Indices: 29403--29487 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
29393 GGCTCGGCTT
*
29403 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
29436 GGCTCGGCTTAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
29469 GGCTCGGCTCAAATGGCTC
1 GGCTCGGCTCAAACGGCTC
29488 CTCAGGCTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:30948 original size:39 final size:39
Alignment explanation
Indices: 30905--30983 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
30895 ACACGCTAAC
30905 ACTTATGTTAGTTTTATAATGACAAAATATCAATTTAAA
1 ACTTATGTTAGTTTTATAATGACAAAATATCAATTTAAA
30944 ACTTATGTTAGTTTTATAATGACAAAATATCAATTTAAA
1 ACTTATGTTAGTTTTATAATGACAAAATATCAATTTAAA
30983 A
1 A
30984 TTTAATCTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (39 bp):
ACTTATGTTAGTTTTATAATGACAAAATATCAATTTAAA
Found at i:40056 original size:14 final size:14
Alignment explanation
Indices: 40037--40076 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
40027 TGGGTTCTTT
40037 TCTCTCTCGCGGCC
1 TCTCTCTCGCGGCC
40051 TCTCTCTCGCGGCC
1 TCTCTCTCGCGGCC
*
40065 TATCTCTCGCGG
1 TCTCTCTCGCGG
40077 AGGGTTGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.03, C:0.45, G:0.23, T:0.30
Consensus pattern (14 bp):
TCTCTCTCGCGGCC
Found at i:41015 original size:14 final size:14
Alignment explanation
Indices: 40996--41022 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40986 CTTCCCGGTT
40996 CGAGGCCATCCGAC
1 CGAGGCCATCCGAC
41010 CGAGGCCATCCGA
1 CGAGGCCATCCGA
41023 GAGCATCCGA
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:0.22, C:0.41, G:0.30, T:0.07
Consensus pattern (14 bp):
CGAGGCCATCCGAC
Found at i:41029 original size:10 final size:9
Alignment explanation
Indices: 41009--41062 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 9
40999 GGCCATCCGA
41009 CCGAGGCCAT
1 CCGAGG-CAT
41019 CCGAGAGCAT
1 CCGAG-GCAT
41029 CCGAGGCTAT
1 CCGAGGC-AT
41039 CCGAGAGCAT
1 CCGAG-GCAT
41049 CCGAGGCCAT
1 CCGAGG-CAT
41059 CCGA
1 CCGA
41063 ACTAGCTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.08
10 34 0.85
11 3 0.08
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (9 bp):
CCGAGGCAT
Found at i:41034 original size:20 final size:20
Alignment explanation
Indices: 41009--41062 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
40999 GGCCATCCGA
41009 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
*
41029 CCGAGGCTATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
41049 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
41063 ACTAGCTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:41082 original size:33 final size:33
Alignment explanation
Indices: 41034--41120 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
41024 AGCATCCGAG
* * * *
41034 GCTATCCGAGAGCATCCGAGGCCATCCGAACTA
1 GCTATGCGAGGGCATCCGAGGCCAACCGAACGA
* *
41067 GCTATGCGAGGGCATCCGAGGGCAACCGAGCGA
1 GCTATGCGAGGGCATCCGAGGCCAACCGAACGA
*
41100 GCTATGCGAGGGAATCCGAGG
1 GCTATGCGAGGGCATCCGAGG
41121 GAAGCCGAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.13
Consensus pattern (33 bp):
GCTATGCGAGGGCATCCGAGGCCAACCGAACGA
Found at i:41121 original size:33 final size:33
Alignment explanation
Indices: 41047--41129 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
41037 ATCCGAGAGC
* * * * *
41047 ATCCGAGGCCATCCGAACTAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
41080 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
41113 ATCCGAGGG-AAGCCGAG
1 ATCCGAGGGCAA-CCGAG
41130 GGTAGGTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 2 0.05
33 42 0.95
ACGTcount: A:0.27, C:0.27, G:0.36, T:0.11
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:41179 original size:29 final size:29
Alignment explanation
Indices: 41133--41246 Score: 192
Period size: 29 Copynumber: 3.9 Consensus size: 29
41123 AGCCGAGGGT
* *
41133 AGGTCACCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
41162 AGGTCGCCAGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
41191 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
41220 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
41247 TGTGTTGGGA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.23, C:0.30, G:0.36, T:0.11
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:41292 original size:12 final size:12
Alignment explanation
Indices: 41275--41299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41265 TGCCATGCAA
41275 CACGTTCATTCT
1 CACGTTCATTCT
41287 CACGTTCATTCT
1 CACGTTCATTCT
41299 C
1 C
41300 TCTGTTTGAG
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:41359 original size:29 final size:29
Alignment explanation
Indices: 41317--41373 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
41307 GAGGAAGGGT
*
41317 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCACCCGGAGTGCATGGCGACCTACA
41346 AGGTCACCCGGAGTGCATGGCGACCTAC
1 AGGTCACCCGGAGTGCATGGCGACCTAC
41374 GGCCAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.32, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCACCCGGAGTGCATGGCGACCTACA
Found at i:42292 original size:13 final size:13
Alignment explanation
Indices: 42274--42332 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
42264 ATTTTAGAAC
42274 TTTCATATTTCAT
1 TTTCATATTTCAT
* *
42287 TTTCATCTATT-AC
1 TTTCATAT-TTCAT
42300 TTTCATA-TTCAT
1 TTTCATATTTCAT
*
42312 TTTCAAATTTCATT
1 TTTCATATTTCA-T
42326 TTTCATA
1 TTTCATA
42333 ACTAGTACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 2 0.06
12 7 0.19
13 18 0.50
14 9 0.25
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTCATATTTCAT
Found at i:42399 original size:19 final size:18
Alignment explanation
Indices: 42363--42432 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 18
42353 GAATTCATTC
* *
42363 TCAGATTCAGAACATATT
1 TCAGATTCATAACTTATT
*
42381 TCCATATTCATAACTTATTT
1 T-CAGATTCATAACTTA-TT
*
42401 TCAGATTCATATCTTAATT
1 TCAGATTCATAACTT-ATT
42420 TCAGATTCATAAC
1 TCAGATTCATAAC
42433 ACAATGCATA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 1 0.02
19 38 0.88
20 4 0.09
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (18 bp):
TCAGATTCATAACTTATT
Found at i:44215 original size:30 final size:30
Alignment explanation
Indices: 44179--44236 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
44169 ATCAAGCCCT
*
44179 TAACTTT-TCAAAATTACCAAATAGATCCCC
1 TAACTTTCACAAAATTA-CAAATAGATCCCC
*
44209 TAACTTTCACAAAATTACAAATTGATCC
1 TAACTTTCACAAAATTACAAATAGATCC
44237 AAATAACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.31
Consensus pattern (30 bp):
TAACTTTCACAAAATTACAAATAGATCCCC
Found at i:44244 original size:31 final size:31
Alignment explanation
Indices: 44179--44247 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
44169 ATCAAGCCCT
* **
44179 TAACTTT-TCAAAATTACCAAATAGATCCCC
1 TAACTTTCACAAAATTACCAAATAGATCCAA
*
44209 TAACTTTCACAAAATTA-CAAATTGATCCAAA
1 TAACTTTCACAAAATTACCAAATAGATCC-AA
44240 TAACTTTC
1 TAACTTTC
44248 TAAAGCTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (31 bp):
TAACTTTCACAAAATTACCAAATAGATCCAA
Found at i:45387 original size:29 final size:29
Alignment explanation
Indices: 45354--45409 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
45344 CCAAATATTT
*
45354 TTTCAAACTTTATACTTTGGCCACTAAAC
1 TTTCAAAATTTATACTTTGGCCACTAAAC
** *
45383 TTTCAAAATTTATGTTTTGGTCACTAA
1 TTTCAAAATTTATACTTTGGCCACTAA
45410 CCATAATTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (29 bp):
TTTCAAAATTTATACTTTGGCCACTAAAC
Found at i:55030 original size:18 final size:18
Alignment explanation
Indices: 55007--55041 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54997 AAAATATGTA
*
55007 TATATATATTTTGAAAAT
1 TATATAAATTTTGAAAAT
55025 TATATAAATTTTGAAAA
1 TATATAAATTTTGAAAA
55042 CATAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATTTTGAAAAT
Found at i:55030 original size:20 final size:22
Alignment explanation
Indices: 54996--55055 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
54986 AATAATTTCA
*
54996 GAAAATATGTATATATATATTTT
1 GAAAACAT-TATATATATATTTT
55019 G-AAA-ATTATATA-A-ATTTT
1 GAAAACATTATATATATATTTT
*
55037 GAAAACATAATATATATAT
1 GAAAACATTATATATATAT
55056 ATATATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 13 0.41
21 3 0.09
22 5 0.16
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (22 bp):
GAAAACATTATATATATATTTT
Found at i:55053 original size:2 final size:2
Alignment explanation
Indices: 55046--55095 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
55036 TGAAAACATA
55046 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
55088 AT AT AT AT
1 AT AT AT AT
55096 GGTTTTGAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55139 original size:23 final size:23
Alignment explanation
Indices: 55109--55174 Score: 107
Period size: 22 Copynumber: 2.9 Consensus size: 23
55099 TTTGAAAATA
55109 GTTTTTGAAAACATATTATATTT
1 GTTTTTGAAAACATATTATATTT
55132 GTTTTTGAAAACATATTATA-TT
1 GTTTTTGAAAACATATTATATTT
* *
55154 GTTTTTGAAAATATAATATAT
1 GTTTTTGAAAACATATTATAT
55175 ATATATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (23 bp):
GTTTTTGAAAACATATTATATTT
Found at i:55212 original size:3 final size:3
Alignment explanation
Indices: 55204--55231 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55194 TATATATACA
55204 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
55232 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:56839 original size:53 final size:53
Alignment explanation
Indices: 56759--56920 Score: 270
Period size: 53 Copynumber: 3.1 Consensus size: 53
56749 GTTGCACCTA
* *
56759 AGTGCCAAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCATACAT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACAT
* * *
56812 AGTGCCGAAATGCTAATTCACAAACTCATTATGAATTCCATGGAGGCACATAT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACAT
*
56865 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGGTGCACACAT
1 AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACAT
56918 AGT
1 AGT
56921 ACTGATACAA
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 100 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (53 bp):
AGTGCCGAAATGGTAATTCACAAACTCATTATGAATTCCATGGATGCACACAT
Found at i:60017 original size:19 final size:19
Alignment explanation
Indices: 59969--60029 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
59959 GAATGCGAAA
59969 TGGTATCGATACCATAGTAGAG
1 TGGTATCGATACCAT-G--GAG
* *
59991 TAGTATCGATACCATGGTG
1 TGGTATCGATACCATGGAG
*
60010 TGGTATCGATACTATGGAG
1 TGGTATCGATACCATGGAG
60029 T
1 T
60030 CAGAAATGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 19 0.56
21 1 0.03
22 14 0.41
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (19 bp):
TGGTATCGATACCATGGAG
Done.