Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007527.1 Hibiscus syriacus cultivar Beakdansim tig00021000_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: 57897
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3598 original size:11 final size:11
Alignment explanation
Indices: 3582--3606 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3572 GAATAGGATT
3582 AAATAAAAATA
1 AAATAAAAATA
3593 AAATAAAAATA
1 AAATAAAAATA
3604 AAA
1 AAA
3607 CAAACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:3763 original size:2 final size:2
Alignment explanation
Indices: 3748--3803 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
3738 ATGTAATGAC
* *
3748 TA TA TA -A TA CA TA TA TA TA TA TA CA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3788 TA TA TA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
3804 GAATAAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:3770 original size:17 final size:17
Alignment explanation
Indices: 3748--3808 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
3738 ATGTAATGAC
*
3748 TATATAATACATATATA
1 TATATAATATATATATA
3765 TATATACATATATA-ATA
1 TATATA-ATATATATATA
3782 TATAT-ATATATATTATA
1 TATATAATATATA-TATA
3799 TATATGAATA
1 TATAT-AATA
3809 AAAGATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 7 0.18
17 22 0.58
18 6 0.16
19 3 0.08
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (17 bp):
TATATAATATATATATA
Found at i:4317 original size:20 final size:20
Alignment explanation
Indices: 4292--4333 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4282 CACGCCGCCT
* * *
4292 CGCCGGCCGCCGTTGATCGG
1 CGCCGGCCACCGATCATCGG
4312 CGCCGGCCACCGATCATCGG
1 CGCCGGCCACCGATCATCGG
4332 CG
1 CG
4334 GCAAACCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.43, G:0.36, T:0.12
Consensus pattern (20 bp):
CGCCGGCCACCGATCATCGG
Found at i:5840 original size:105 final size:105
Alignment explanation
Indices: 5548--6115 Score: 877
Period size: 105 Copynumber: 5.4 Consensus size: 105
5538 GTATTGTTCC
* *** * * * * *
5548 GAGTCCAATATCCTCCACCGTGGAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * ** *
5613 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGGAGTCCG
65 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5654 GAGTCCAATATCCTTCGTTGTGAAGTTGAAAATTGGCTCTGAGATTGAGAAATGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTG-AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
5719 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5760 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATGGAGAAATGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
5825 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5865 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
5930 CAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5970 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
6035 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
6075 GAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
6116 GTAAAACCTG
Statistics
Matches: 426, Mismatches: 34, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
105 312 0.73
106 96 0.23
107 18 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:6599 original size:67 final size:66
Alignment explanation
Indices: 6464--6621 Score: 201
Period size: 68 Copynumber: 2.4 Consensus size: 66
6454 AAGATATCTG
* * **
6464 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTTAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA-
6529 TT
65 TT
* * * * *
6531 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
6595 TT
65 TT
*
6597 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
6622 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 22 0.28
66 3 0.04
67 23 0.29
68 31 0.39
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:6637 original size:65 final size:67
Alignment explanation
Indices: 6465--6647 Score: 183
Period size: 65 Copynumber: 2.7 Consensus size: 67
6455 AGATATCTGT
* * * * * ** *
6465 TGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTTAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAGT
6530 TTG
65 TTG
* * * *
6533 TGTTTCAAGAGTAACTGTCTCAAGGGAGATAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
6597 T-
66 TG
* * * *
6598 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-GAAAATTTGTTTTAAGGGAAA
6648 CTGTCTCAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 37 0.38
66 7 0.07
67 22 0.23
68 31 0.32
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:6648 original size:36 final size:35
Alignment explanation
Indices: 6597--6875 Score: 268
Period size: 36 Copynumber: 8.0 Consensus size: 35
6587 TTCAAAGGTT
* *
6597 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
6633 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
6668 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * * **
6706 TTGTTTCAA-AGAAAAC-ATATC---A-A-A-TATT
1 TTGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA
*
6734 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
6769 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
6806 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
6841 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
6876 CTCTTCTAGT
Statistics
Matches: 200, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
28 15 0.08
29 4 0.02
30 1 0.00
31 1 0.00
32 1 0.00
33 1 0.00
34 1 0.00
35 46 0.23
36 97 0.49
37 31 0.16
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:6792 original size:137 final size:135
Alignment explanation
Indices: 6595--6849 Score: 368
Period size: 137 Copynumber: 1.9 Consensus size: 135
6585 AATTCAAAGG
* *
6595 TTTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAATTATTTCAAGAGAAACTGTCTCAAGAG
* * * *
6660 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATA
66 AGACAAAA-TTAGTTCCAAAAGAAACTATCTCAAGAGAGAC-AAAATTGTTTCAAAGAAAACATA
6725 TCAAATA
129 TCAAATA
*
6732 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGGGAAACTGTCTCAAGA
1 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAA-TTATTTCAAGAGAAACTGTCTCAAGA
* * * * *
6796 TAGACGAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTGTTTCAA
65 GAGACAAAATTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTGTTTCAA
6850 GGGAAACTGT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
135 11 0.10
136 31 0.30
137 63 0.60
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (135 bp):
TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAATTATTTCAAGAGAAACTGTCTCAAGAG
AGACAAAATTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTGTTTCAAAGAAAACATATC
AAATA
Found at i:6820 original size:101 final size:105
Alignment explanation
Indices: 6596--6877 Score: 315
Period size: 101 Copynumber: 2.7 Consensus size: 105
6586 ATTCAAAGGT
* * * *
6596 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAATTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAA-AGAAACTATATCAAG--AGAC-AAAATTGTTTCAAGGGAAACTGTCTCAAGAGA
* *
6661 GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAA
62 GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAA
* **
6705 TTTGTTTCAAAGAAAAC-ATATC-A-A-A-TATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTTGTTTCAAAG-AAACTATATCAAGAGACAAAATTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * ** *
6765 AAAATTTA-TTTCAAGGGAAACTGTCTCAAGATAGACGAAA
65 AAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAA
*
6805 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TTTGTTTCAA-AGAAACTATATC-A-AGAGACAAAATTGTTTCAAGGGAAACTGTCTCAAGAGAG
6870 ACAAAACT
63 ACAAAACT
6878 CTTCTAGTGA
Statistics
Matches: 145, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
100 40 0.28
101 44 0.30
103 1 0.01
104 2 0.01
105 1 0.01
106 1 0.01
107 38 0.26
108 4 0.03
109 14 0.10
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (105 bp):
TTTGTTTCAAAGAAACTATATCAAGAGACAAAATTGTTTCAAGGGAAACTGTCTCAAGAGAGACA
AAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAA
Found at i:6897 original size:35 final size:35
Alignment explanation
Indices: 6738--6909 Score: 123
Period size: 35 Copynumber: 4.9 Consensus size: 35
6728 AATATTTTGT
* * * **
6738 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACGGTCTCAAGAGAGACAAAA-CTGC
* * * ** *
6774 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACGGTCTCAAGAGAGAC-AAAACTGC
** * *
6810 TTCAA-GAGAAACTATCTCAAGAGAGACAAAATTGT
1 TTCAAGGA-AAACGGTCTCAAGAGAGACAAAACTGC
* *
6845 TTCAAGGGAAACTGTCTCAAGAGAGACAAAACT-C
1 TTCAAGGAAAACGGTCTCAAGAGAGACAAAACTGC
* *
6879 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACGGTCTCAAGAGAGACAAA
6910 TCTTGTTTAA
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
34 5 0.04
35 57 0.49
36 52 0.44
37 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (35 bp):
TTCAAGGAAAACGGTCTCAAGAGAGACAAAACTGC
Found at i:6916 original size:71 final size:71
Alignment explanation
Indices: 6738--6917 Score: 211
Period size: 71 Copynumber: 2.5 Consensus size: 71
6728 AATATTTTGT
* * *
6738 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGAC-AAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
** *
6803 AATTTGT
65 AAACTGC
* *
6810 TTCAAGAGAAACTATCTCAAGAGAGACAAAATTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAA
6874 AACT-C
66 AACTGC
* * * *
6879 TTCTAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTT
1 TTCAAGAG-AAACTGTCTCAAGAGAGACAAAT-TTGTTT
6918 AAGAAAAACA
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
69 6 0.07
70 23 0.25
71 38 0.41
72 25 0.27
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (71 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAA
AACTGC
Found at i:7828 original size:22 final size:22
Alignment explanation
Indices: 7802--7850 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
7792 TTGTGTTTGG
* *
7802 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
7824 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
7846 TCAAA
1 TCAAA
7851 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:7857 original size:22 final size:22
Alignment explanation
Indices: 7814--7857 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
7804 AAAGGTTTGG
* * *
7814 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
7836 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
7858 TGGGGTAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:8510 original size:23 final size:23
Alignment explanation
Indices: 8484--8579 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 23
8474 TTTTTGTCCC
*
8484 TTTTTCTTTTGATTTTTGCTCTT
1 TTTTTCTTTTGTTTTTTGCTCTT
*
8507 TTTTTCTTTTGTTCTTGTTTCTCTT
1 TTTTTCTTTTGTT-TT-TTGCTCTT
* *
8532 TTTCTT-TGTTTTTTTTTTGCTTTT
1 TTT-TTCT-TTTGTTTTTTGCTCTT
* *
8556 TTGTTTCTTTTCTTTTTTGTTCTT
1 TT-TTTCTTTTGTTTTTTGCTCTT
8580 GATTGGATCT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
23 12 0.20
24 25 0.42
25 15 0.25
26 7 0.12
ACGTcount: A:0.01, C:0.12, G:0.08, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTGTTTTTTGCTCTT
Found at i:8514 original size:8 final size:8
Alignment explanation
Indices: 8503--8573 Score: 58
Period size: 8 Copynumber: 9.0 Consensus size: 8
8493 TGATTTTTGC
8503 TCTTTTTT
1 TCTTTTTT
*
8511 TCTTTTGT
1 TCTTTTTT
*
8519 TC-TTGTT
1 TCTTTTTT
*
8526 TCTCTTTT
1 TCTTTTTT
8534 TCTTTGTTT
1 TCTTT-TTT
8543 T-TTTTTT
1 TCTTTTTT
*
8550 GCTTTTTT
1 TCTTTTTT
*
8558 GT-TTCTTT
1 -TCTTTTTT
8566 TCTTTTTT
1 TCTTTTTT
8574 GTTCTTGATT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
7 9 0.19
8 35 0.73
9 4 0.08
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:8516 original size:16 final size:15
Alignment explanation
Indices: 8497--8579 Score: 62
Period size: 17 Copynumber: 5.1 Consensus size: 15
8487 TTCTTTTGAT
8497 TTTTGCTCTTTTTTTC
1 TTTTGCT-TTTTTTTC
8513 TTTTG-TTCTTGTTTCTC
1 TTTTGCTT-TT-TTT-TC
* *
8530 TTTTTCTTTGTTTTTT
1 TTTTGCTTT-TTTTTC
8546 TTTTGCTTTTTTGTTTC
1 TTTTGC-TTTTT-TTTC
8563 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTT-TTC
8578 TT
1 TT
8580 GATTGGATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
14 2 0.04
15 13 0.24
16 17 0.31
17 20 0.36
18 3 0.05
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.78
Consensus pattern (15 bp):
TTTTGCTTTTTTTTC
Found at i:8554 original size:22 final size:23
Alignment explanation
Indices: 8530--8574 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
8520 CTTGTTTCTC
8530 TTTTTCTTTGTTTTTTTTTTGCT
1 TTTTTCTTTGTTTTTTTTTTGCT
* *
8553 TTTTTGTTTCTTTTCTTTTTTG
1 TTTTTCTTTGTTTT-TTTTTTG
8575 TTCTTGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTGTTTTTTTTTTGCT
Found at i:11922 original size:2 final size:2
Alignment explanation
Indices: 11915--11964 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
11905 ATAATAATAC
*
11915 AT AT AT AT AC 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
11957 AT AT AT AT
1 AT AT AT AT
11965 GAAAATAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12092 original size:21 final size:21
Alignment explanation
Indices: 12046--12098 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
12036 TGATATATAC
* *
12046 AAAAATAATAATATTAATATT
1 AAAAATAATAATAATAATAGT
* *
12067 GAAAATAATAATAATAATGGT
1 AAAAATAATAATAATAATAGT
*
12088 AAAAAAAATAA
1 AAAAATAATAA
12099 AAGAAAGTGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (21 bp):
AAAAATAATAATAATAATAGT
Found at i:12493 original size:20 final size:20
Alignment explanation
Indices: 12468--12509 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12458 CACGCCGCCT
* * *
12468 CGCCGGCCGCCGTTGATCGG
1 CGCCGGCCACCGATCATCGG
12488 CGCCGGCCACCGATCATCGG
1 CGCCGGCCACCGATCATCGG
12508 CG
1 CG
12510 GCAAACCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.43, G:0.36, T:0.12
Consensus pattern (20 bp):
CGCCGGCCACCGATCATCGG
Found at i:21719 original size:27 final size:27
Alignment explanation
Indices: 21681--21735 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
21671 AGGAAAACAC
21681 TTGCAGCCAAACACTTTCATCAAATTA
1 TTGCAGCCAAACACTTTCATCAAATTA
21708 TTGCAGCCAAACACTTTCATCAAATTA
1 TTGCAGCCAAACACTTTCATCAAATTA
21735 T
1 T
21736 AGTCTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (27 bp):
TTGCAGCCAAACACTTTCATCAAATTA
Found at i:24700 original size:21 final size:21
Alignment explanation
Indices: 24674--24713 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24664 TCCGAGTTAC
*
24674 CCACGACGGCCGCAATAGCGT
1 CCACGACGACCGCAATAGCGT
*
24695 CCACGATGACCGCAATAGC
1 CCACGACGACCGCAATAGC
24714 ACCCGTGACG
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:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
CCACGACGACCGCAATAGCGT
Found at i:25411 original size:22 final size:21
Alignment explanation
Indices: 25386--25446 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
25376 AATATATATT
25386 TATATAAATATATATTTATTCATA
1 TATATAAATATAT-TTTATT-A-A
* *
25410 TATTTAAATAT-TTTTGTTAA
1 TATATAAATATATTTTATTAA
*
25430 AATATAAATATATTTTA
1 TATATAAATATATTTTA
25447 AATATTAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.32
21 5 0.16
22 5 0.16
23 1 0.03
24 10 0.32
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TATATAAATATATTTTATTAA
Found at i:33445 original size:43 final size:45
Alignment explanation
Indices: 33341--33446 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 45
33331 AGGATTAGAT
*
33341 TTATTATTTTATTAGGAATTAAGGTTGAGTTAAAACATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTTAAAAC--TATCTTTAGTTA
*
33391 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-ATCTTTAGTTTG
1 TTATTATTTTATTAGGAATTAAGGAGTTAAAACTATCTTTAG-TTA
33434 TTATTATTTTATT
1 TTATTATTTTATT
33447 CATTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 7 0.13
43 15 0.28
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAAACTATCTTTAGTTA
Found at i:37863 original size:23 final size:20
Alignment explanation
Indices: 37816--37863 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
37806 AATAGTGTTA
37816 TATTATATTTTTAAAATATT
1 TATTATATTTTTAAAATATT
* *
37836 AATTAGTATATTTTAAATATCTT
1 TATTA-TAT-TTTTAAA-ATATT
37859 TATTA
1 TATTA
37864 AAATATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 7 0.32
23 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTATATTTTTAAAATATT
Found at i:37926 original size:19 final size:19
Alignment explanation
Indices: 37858--37938 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
37848 TTAAATATCT
37858 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
37877 TTATTAGATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
37896 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
37916 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
37934 -TATTA
1 TTATTA
37939 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:39729 original size:28 final size:28
Alignment explanation
Indices: 39689--39751 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
39679 CATACATGAT
39689 ATTAAAAAACAAAACATAACCATTTAAG
1 ATTAAAAAACAAAACATAACCATTTAAG
39717 ATTAAAAAACAAAACATAACCATTTAAG
1 ATTAAAAAACAAAACATAACCATTTAAG
39745 ATTAAAA
1 ATTAAAA
39752 CTCATGCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.62, C:0.13, G:0.03, T:0.22
Consensus pattern (28 bp):
ATTAAAAAACAAAACATAACCATTTAAG
Found at i:42516 original size:23 final size:23
Alignment explanation
Indices: 42490--42564 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
42480 CAAAAATAAA
*
42490 AATATTATACCTTATATTATTAT
1 AATATTATACATTATATTATTAT
* ** *
42513 AATATAATTGATTATTTTATTAT
1 AATATTATACATTATATTATTAT
* * *
42536 AATATTA-AAAATATAATATTAT
1 AATATTATACATTATATTATTAT
*
42558 ATTATTA
1 AATATTA
42565 GAAATATTAA
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
22 16 0.40
23 24 0.60
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (23 bp):
AATATTATACATTATATTATTAT
Found at i:42558 original size:22 final size:23
Alignment explanation
Indices: 42530--42576 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
42520 TTGATTATTT
42530 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
42552 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
42575 TA
1 TA
42577 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:42581 original size:22 final size:22
Alignment explanation
Indices: 42538--42581 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42528 TTTATTATAA
*
42538 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
42560 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
42582 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:42859 original size:14 final size:14
Alignment explanation
Indices: 42824--42857 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42814 TAGAAAATGA
*
42824 GGAAAACATTTTCC
1 GGAAAACATTTTAC
42838 GGAAAACATTTTAC
1 GGAAAACATTTTAC
42852 GTGAAA
1 G-GAAA
42858 CAAAAGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (14 bp):
GGAAAACATTTTAC
Found at i:44496 original size:16 final size:16
Alignment explanation
Indices: 44477--44508 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
44467 AAAAATTAAA
44477 TTAATGGTGCTCATCG
1 TTAATGGTGCTCATCG
44493 TTAATGGTGCTCATCG
1 TTAATGGTGCTCATCG
44509 CTGCTTATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
TTAATGGTGCTCATCG
Found at i:44725 original size:20 final size:20
Alignment explanation
Indices: 44702--44741 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44692 TAGATTTTAA
44702 TAAAAA-AAATACATAATTTT
1 TAAAAATAAATA-ATAATTTT
*
44722 TAAAAATATATAATAATTTT
1 TAAAAATAAATAATAATTTT
44742 AAATTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAATAAATAATAATTTT
Found at i:45757 original size:34 final size:34
Alignment explanation
Indices: 45714--45781 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
45704 TAAACTACGC
45714 ATTTAATACTTAAACTATCAGTTTCGTTTTTTTA
1 ATTTAATACTTAAACTATCAGTTTCGTTTTTTTA
45748 ATTTAATACTTAAACTATCAGTTTCGTTTTTTTA
1 ATTTAATACTTAAACTATCAGTTTCGTTTTTTTA
45782 GTATCTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (34 bp):
ATTTAATACTTAAACTATCAGTTTCGTTTTTTTA
Found at i:46235 original size:2 final size:2
Alignment explanation
Indices: 46228--46262 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
46218 CCTACCTACC
46228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46263 TTAGTCTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48261 original size:28 final size:30
Alignment explanation
Indices: 48223--48281 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
48213 TTATATAATT
*
48223 TATTATTTTATT-AATATTAA-AAATATAA
1 TATTATATTATTAAATATTAATAAATATAA
48251 TATTATATTATTAGAAATATTAATAAATATA
1 TATTATATTATT--AAATATTAATAAATATA
48282 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 11 0.42
31 8 0.31
32 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TATTATATTATTAAATATTAATAAATATAA
Found at i:48280 original size:22 final size:22
Alignment explanation
Indices: 48237--48280 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
48227 ATTTTATTAA
*
48237 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
48259 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
48281 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:48558 original size:14 final size:14
Alignment explanation
Indices: 48523--48556 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
48513 TGGAAAATGA
*
48523 GGAAAACATTTTCC
1 GGAAAACATTTTAC
48537 GGAAAACATTTTAC
1 GGAAAACATTTTAC
48551 GTGAAA
1 G-GAAA
48557 CAAAAGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (14 bp):
GGAAAACATTTTAC
Found at i:53720 original size:21 final size:21
Alignment explanation
Indices: 53696--53738 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53686 TCTCATGTTA
* *
53696 GTAGTTTCGATCTAGCATGAG
1 GTAGTTTCGAGCTAACATGAG
53717 GTAGTTTCGAGCTAACATGAG
1 GTAGTTTCGAGCTAACATGAG
53738 G
1 G
53739 AAGAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (21 bp):
GTAGTTTCGAGCTAACATGAG
Found at i:54172 original size:3 final size:3
Alignment explanation
Indices: 54160--54252 Score: 90
Period size: 3 Copynumber: 32.0 Consensus size: 3
54150 TCATTTGTTT
* *
54160 TTA TTA -TA TTA TTA TTA TTG TT- TTA TT- TTA TTTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
54203 TT- TTA TTA -TA TTA TTA TTA TTA TTA ATA -TA TATA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT-A TTA
54247 TTA TTA
1 TTA TTA
54253 CAGGCCAAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
2 12 0.16
3 56 0.73
4 9 0.12
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54194 original size:23 final size:22
Alignment explanation
Indices: 54158--54251 Score: 116
Period size: 22 Copynumber: 4.1 Consensus size: 22
54148 ATTCATTTGT
*
54158 TTTTATTATATTATTATTATTG
1 TTTTATTATATTATTATTATTA
* *
54180 TTTTATTTTATTTATCATTATTA
1 TTTTATTATA-TTATTATTATTA
54203 TTTTATTATATTATTATTATTA
1 TTTTATTATATTATTATTATTA
*
54225 TTAATATATATATTATTAATTATTA
1 TT-TTAT-TATATTATT-ATTATTA
54250 TT
1 TT
54252 ACAGGCCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
22 22 0.35
23 22 0.35
24 9 0.15
25 9 0.15
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTTATTATATTATTATTATTA
Found at i:54240 original size:15 final size:13
Alignment explanation
Indices: 54160--54252 Score: 79
Period size: 14 Copynumber: 7.2 Consensus size: 13
54150 TCATTTGTTT
54160 TTATTATATTATTA
1 TTATTA-ATTATTA
*
54174 TTATT-GTT-TTA
1 TTATTAATTATTA
* *
54185 TT-TTATTTATCA
1 TTATTAATTATTA
54197 TTATT-ATT-TTA
1 TTATTAATTATTA
*
54208 TTATATTATTATTA
1 TTAT-TAATTATTA
54222 TTATTAATATATATA
1 TTATTAAT-TAT-TA
54237 TTATTAATTATTA
1 TTATTAATTATTA
54250 TTA
1 TTA
54253 CAGGCCAAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.03
11 13 0.20
12 9 0.14
13 13 0.20
14 18 0.28
15 10 0.15
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (13 bp):
TTATTAATTATTA
Found at i:55755 original size:21 final size:21
Alignment explanation
Indices: 55712--55753 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55702 TCCTATTTAA
* *
55712 TAATTATATATATATCTGCTT
1 TAATTATATATAAATCTACTT
55733 TAATTATATATAAAT-TACTT
1 TAATTATATATAAATCTACTT
55753 T
1 T
55754 TAGGGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATTATATATAAATCTACTT
Done.