Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002877.1 Hibiscus syriacus cultivar Beakdansim tig00005931_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: 291049
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:212708 original size:42 final size:42
Alignment explanation
Indices: 212657--212822 Score: 192
Period size: 42 Copynumber: 4.0 Consensus size: 42
212647 GCAATAGAGT
* * * *
212657 AGTACTTTAGTGGTGTTTGTGCTTAAAACGCCTCTAAAGTACG
1 AGTA-TTTAGTGGCGTTTGTACTTAAAATGCCACTAAAGTACG
* * *
212700 AGTATTTAGTGGCGTTTTTGCTTAAAATGCCACTAAAGTACT
1 AGTATTTAGTGGCGTTTGTACTTAAAATGCCACTAAAGTACG
* * * * *
212742 AGTCTTTAGCGGCGTTTGTAC-AAAAATGCCACGAAAGTATG
1 AGTATTTAGTGGCGTTTGTACTTAAAATGCCACTAAAGTACG
*
212783 AGT-TTTAGTGGCGTTTATACTTAAAATGCCACTAAAGTAC
1 AGTATTTAGTGGCGTTTGTACTTAAAATGCCACTAAAGTAC
212823 TACTCTATTG
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 15 0.14
41 35 0.34
42 50 0.48
43 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (42 bp):
AGTATTTAGTGGCGTTTGTACTTAAAATGCCACTAAAGTACG
Found at i:212780 original size:41 final size:41
Alignment explanation
Indices: 212681--212824 Score: 148
Period size: 41 Copynumber: 3.5 Consensus size: 41
212671 GTTTGTGCTT
* * * * * * *
212681 AAAACGCCTCTAAAGTACGAGTATTTAGTGGCGTTTTTGCTT
1 AAAATGCCACTAAAGTACTAGT-TTTAGCGGCGTTTATACTA
*
212723 AAAATGCCACTAAAGTACTAGTCTTTAGCGGCGTTTGTAC-A
1 AAAATGCCACTAAAGTACTAGT-TTTAGCGGCGTTTATACTA
* * *
212764 AAAATGCCACGAAAGTA-TGAGTTTTAGTGGCGTTTATACTT
1 AAAATGCCACTAAAGTACT-AGTTTTAGCGGCGTTTATACTA
212805 AAAATGCCACTAAAGTACTA
1 AAAATGCCACTAAAGTACTA
212825 CTCTATTGCG
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
40 16 0.19
41 36 0.42
42 34 0.40
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (41 bp):
AAAATGCCACTAAAGTACTAGTTTTAGCGGCGTTTATACTA
Found at i:213713 original size:44 final size:44
Alignment explanation
Indices: 213650--213737 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
213640 TTAGAGATTT
213650 TGCCGGAAAAACCTGTCACCTTCGTAAAGACACACCCTACAAAC
1 TGCCGGAAAAACCTGTCACCTTCGTAAAGACACACCCTACAAAC
*
213694 TGCCGGAAAAACCTGTCACCTTCGTAAGGACACACCCTACAAAC
1 TGCCGGAAAAACCTGTCACCTTCGTAAAGACACACCCTACAAAC
213738 CGCGTCTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.34, G:0.15, T:0.16
Consensus pattern (44 bp):
TGCCGGAAAAACCTGTCACCTTCGTAAAGACACACCCTACAAAC
Found at i:216451 original size:15 final size:15
Alignment explanation
Indices: 216431--216459 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
216421 GATCAAGGAA
216431 ACAGATGAAGAAGAC
1 ACAGATGAAGAAGAC
216446 ACAGATGAAGAAGA
1 ACAGATGAAGAAGA
216460 AATAGAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.28, T:0.07
Consensus pattern (15 bp):
ACAGATGAAGAAGAC
Found at i:216919 original size:21 final size:21
Alignment explanation
Indices: 216895--216944 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
216885 GGCTAGGGGG
216895 CATAAGTTGCACAGCCGGTGC
1 CATAAGTTGCACAGCCGGTGC
216916 CATAAGTTGCACAGCCGGTGC
1 CATAAGTTGCACAGCCGGTGC
216937 CATAAGTT
1 CATAAGTT
216945 TCAATGGCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (21 bp):
CATAAGTTGCACAGCCGGTGC
Found at i:225603 original size:10 final size:10
Alignment explanation
Indices: 225584--225661 Score: 74
Period size: 10 Copynumber: 8.2 Consensus size: 10
225574 GTAATTGATG
*
225584 CATATGCATA
1 CATATACATA
225594 CATATACATA
1 CATATACATA
* *
225604 TATATACATG
1 CATATACATA
225614 C--AT--ATA
1 CATATACATA
225620 CATATACATA
1 CATATACATA
* *
225630 TATATACATG
1 CATATACATA
225640 CATATACATA
1 CATATACATA
*
225650 TATATACATA
1 CATATACATA
225660 CA
1 CA
225662 CTCACACATA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
6 3 0.06
8 4 0.08
10 46 0.87
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (10 bp):
CATATACATA
Found at i:225617 original size:20 final size:21
Alignment explanation
Indices: 225596--225677 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 21
225586 TATGCATACA
225596 TATACATATATATACATGCATATAC
1 TATACATATATATACATGC----AC
225621 ATATACATATATATACATGCA-
1 -TATACATATATATACATGCAC
*
225642 TATACATATATATACATACAC
1 TATACATATATATACATGCAC
*
225663 TCACACATATATATA
1 T-ATACATATATATA
225678 GATTGTGTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
20 19 0.37
21 1 0.02
22 13 0.25
26 19 0.37
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.34
Consensus pattern (21 bp):
TATACATATATATACATGCAC
Found at i:225623 original size:26 final size:26
Alignment explanation
Indices: 225591--225651 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
225581 ATGCATATGC
225591 ATACATATACATATATATACATGCAT
1 ATACATATACATATATATACATGCAT
225617 ATACATATACATATATATACATGCAT
1 ATACATATACATATATATACATGCAT
225643 ATACATATA
1 ATACATATA
225652 TATACATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (26 bp):
ATACATATACATATATATACATGCAT
Found at i:228758 original size:3 final size:3
Alignment explanation
Indices: 228743--228830 Score: 59
Period size: 3 Copynumber: 29.0 Consensus size: 3
228733 ACCTTGGGTC
* * * * * * *
228743 CTT CTT ATT CTT CTT CTC CTC CTC CTC CTT CTT CTT CTC CTC CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * *
228791 CTC CTC CTC CTT CTT CTT CTC CTC CTT CTT CTT CTAT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT
228831 TCACTGTCGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
3 71 0.96
4 3 0.04
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.53
Consensus pattern (3 bp):
CTT
Found at i:228765 original size:21 final size:21
Alignment explanation
Indices: 228741--228790 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
228731 CTACCTTGGG
228741 TCCTTCTTATTCTTCTTCTCC
1 TCCTTCTTATTCTTCTTCTCC
* **
228762 TCCTCCTCCTTCTTCTTCTCC
1 TCCTTCTTATTCTTCTTCTCC
228783 TCCTTCTT
1 TCCTTCTT
228791 CTCCTCCTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (21 bp):
TCCTTCTTATTCTTCTTCTCC
Found at i:228782 original size:15 final size:15
Alignment explanation
Indices: 228764--228825 Score: 115
Period size: 15 Copynumber: 4.1 Consensus size: 15
228754 TCTTCTCCTC
228764 CTCCTCCTTCTTCTT
1 CTCCTCCTTCTTCTT
*
228779 CTCCTCCTTCTTCTC
1 CTCCTCCTTCTTCTT
228794 CTCCTCCTTCTTCTT
1 CTCCTCCTTCTTCTT
228809 CTCCTCCTTCTTCTT
1 CTCCTCCTTCTTCTT
228824 CT
1 CT
228826 ATCTTTCACT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CTCCTCCTTCTTCTT
Found at i:228820 original size:30 final size:30
Alignment explanation
Indices: 228755--228822 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
228745 TCTTATTCTT
*
228755 CTTCTCCTCCTCCTCCTTCTTCTTCTCCTC
1 CTTCTTCTCCTCCTCCTTCTTCTTCTCCTC
228785 CTTCTTCTCCTCCTCCTTCTTCTTCTCCTC
1 CTTCTTCTCCTCCTCCTTCTTCTTCTCCTC
228815 CTTCTTCT
1 CTTCTTCT
228823 TCTATCTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (30 bp):
CTTCTTCTCCTCCTCCTTCTTCTTCTCCTC
Found at i:228821 original size:18 final size:18
Alignment explanation
Indices: 228750--228825 Score: 104
Period size: 18 Copynumber: 4.4 Consensus size: 18
228740 GTCCTTCTTA
228750 TTCTTCTTCTCCTCCTCC
1 TTCTTCTTCTCCTCCTCC
*
228768 TCCTTCTTCT--T-CTCC
1 TTCTTCTTCTCCTCCTCC
*
228783 TCCTTCTTCTCCTCCTCC
1 TTCTTCTTCTCCTCCTCC
*
228801 TTCTTCTTCTCCTCCTTC
1 TTCTTCTTCTCCTCCTCC
228819 TTCTTCT
1 TTCTTCT
228826 ATCTTTCACT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
15 14 0.27
16 1 0.02
17 1 0.02
18 36 0.69
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (18 bp):
TTCTTCTTCTCCTCCTCC
Found at i:229062 original size:22 final size:22
Alignment explanation
Indices: 229036--229081 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
229026 AAAGGGGAAA
229036 GGCGAAAGGAGTGAATC-AAGCC
1 GGCGAAAGGAGTGAA-CGAAGCC
*
229058 GGCGAAGGGAGTGAACGAAGCC
1 GGCGAAAGGAGTGAACGAAGCC
229080 GG
1 GG
229082 TTTTGGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.33, C:0.17, G:0.43, T:0.07
Consensus pattern (22 bp):
GGCGAAAGGAGTGAACGAAGCC
Found at i:233849 original size:30 final size:30
Alignment explanation
Indices: 233813--233881 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
233803 TATTCTAATG
233813 TTGCTGCT-ACTAAGAACAAAACTGAAGTTA
1 TTGCTGCTGACT-AGAACAAAACTGAAGTTA
* * *
233843 TTGCTGCTGTCTCGAACAAAGCTGAAGTTA
1 TTGCTGCTGACTAGAACAAAACTGAAGTTA
*
233873 CTGCTGCTG
1 TTGCTGCTG
233882 GCACGATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.94
31 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (30 bp):
TTGCTGCTGACTAGAACAAAACTGAAGTTA
Found at i:233908 original size:30 final size:30
Alignment explanation
Indices: 233826--233910 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
233816 CTGCTACTAA
* * *
233826 GAACAAAACTGAAGTTATTGCTGCTGTCTC
1 GAACAAAGCTGAAGTTATTGCTGCTGGCAC
*
233856 GAACAAAGCTGAAGTTACTGCTGCTGGCAC
1 GAACAAAGCTGAAGTTATTGCTGCTGGCAC
* *
233886 GATCAAAGCTGATA-TTGTTGCTGCT
1 GAACAAAGCTGA-AGTTATTGCTGCT
233911 CTTAAGAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (30 bp):
GAACAAAGCTGAAGTTATTGCTGCTGGCAC
Found at i:240547 original size:14 final size:14
Alignment explanation
Indices: 240528--240579 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
240518 CGGTCGATAA
*
240528 TATATTCGTTCATT
1 TATATTCGTTCGTT
240542 TATATTCGTTCGTT
1 TATATTCGTTCGTT
* * *
240556 TATGTTCATTTGTT
1 TATATTCGTTCGTT
240570 TATATTCGTT
1 TATATTCGTT
240580 TATGTTTAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (14 bp):
TATATTCGTTCGTT
Found at i:240803 original size:17 final size:17
Alignment explanation
Indices: 240781--240822 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
240771 TACGTTCTTT
240781 TATGTTCATTTATTGTG
1 TATGTTCATTTATTGTG
240798 TATGTTCATTTATTGTG
1 TATGTTCATTTATTGTG
*
240815 TACGTTCA
1 TATGTTCA
240823 CGGTCGTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.55
Consensus pattern (17 bp):
TATGTTCATTTATTGTG
Found at i:251428 original size:25 final size:25
Alignment explanation
Indices: 251394--251445 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
251384 AGGTATTTTA
251394 TTTTCGAGATAATATAATACCTTTG
1 TTTTCGAGATAATATAATACCTTTG
* *
251419 TTTTCTAGATAATATGATACCTTTG
1 TTTTCGAGATAATATAATACCTTTG
251444 TT
1 TT
251446 GGCGCAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (25 bp):
TTTTCGAGATAATATAATACCTTTG
Found at i:252644 original size:60 final size:59
Alignment explanation
Indices: 252490--252644 Score: 168
Period size: 59 Copynumber: 2.6 Consensus size: 59
252480 ATGAAAGATC
* * * * **
252490 TAAAATTTTAGGGACCAATTTATAATGAGATTCATAGTTTCAGGATGAAAATGGAATGT
1 TAAAAATTTAGAGACCAATTTAAAATGAGATTCATAGTTTAAGGATGAAAATAAAATGT
* * * * *
252549 TAAAAATTTA-AGGACTAATTTAGAATGATATTCATAGTTTAAGGATGAAATTAAAATATT
1 TAAAAATTTAGA-GACCAATTTAAAATGAGATTCATAGTTTAAGGATGAAAATAAAAT-GT
* *
252609 TAAAAGTTTAGAGACCAATTTAAAATGAGAGTCATA
1 TAAAAATTTAGAGACCAATTTAAAATGAGATTCATA
252645 ATTAGGAGAC
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 47 0.60
60 30 0.38
61 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (59 bp):
TAAAAATTTAGAGACCAATTTAAAATGAGATTCATAGTTTAAGGATGAAAATAAAATGT
Found at i:253131 original size:20 final size:22
Alignment explanation
Indices: 253097--253137 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
253087 AAAAACGTAA
*
253097 AAAATAATATTTAAA-AATTAG
1 AAAATAATATCTAAATAATTAG
253118 AAAA-AATATCTAAATAATTA
1 AAAATAATATCTAAATAATTA
253138 ATGAAGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATAATATCTAAATAATTAG
Found at i:260176 original size:16 final size:16
Alignment explanation
Indices: 260137--260203 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
260127 GACTGATACA
* *
260137 AATTTGAACAAAAAAT
1 AATTTGAACCAAAAGT
** *
260153 AACATGAAGCAAAAGT
1 AATTTGAACCAAAAGT
*
260169 AATTTGAACCGAAAGT
1 AATTTGAACCAAAAGT
* *
260185 AACTTGAATCAAAAGT
1 AATTTGAACCAAAAGT
260201 AAT
1 AAT
260204 ATGTTGAGTT
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTTGAACCAAAAGT
Found at i:260198 original size:32 final size:32
Alignment explanation
Indices: 260137--260203 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
260127 GACTGATACA
260137 AATTTGAACAAAAAATAACATGAAGCAAAAGT
1 AATTTGAACAAAAAATAACATGAAGCAAAAGT
** * * *
260169 AATTTGAACCGAAAGTAACTTGAATCAAAAGT
1 AATTTGAACAAAAAATAACATGAAGCAAAAGT
260201 AAT
1 AAT
260204 ATGTTGAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (32 bp):
AATTTGAACAAAAAATAACATGAAGCAAAAGT
Found at i:261381 original size:20 final size:20
Alignment explanation
Indices: 261356--261395 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
261346 CCTTACTTTA
261356 ACACTACTCCTCAAAAACGC
1 ACACTACTCCTCAAAAACGC
261376 ACACTACTCCTCAAAAACGC
1 ACACTACTCCTCAAAAACGC
261396 TTTTATCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.05, T:0.15
Consensus pattern (20 bp):
ACACTACTCCTCAAAAACGC
Found at i:262527 original size:24 final size:24
Alignment explanation
Indices: 262483--262532 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
262473 ATAAAGAACC
*
262483 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
262507 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
262531 AA
1 AA
262533 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:269335 original size:21 final size:21
Alignment explanation
Indices: 269305--269348 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
269295 AGACGAGCTA
* *
269305 TGGCTTTGAAGTAAGGCGCCT
1 TGGCTATGAAGTAAAGCGCCT
*
269326 TGGCTATGAAGTAAAGCTCCT
1 TGGCTATGAAGTAAAGCGCCT
269347 TG
1 TG
269349 ATTCTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (21 bp):
TGGCTATGAAGTAAAGCGCCT
Found at i:271673 original size:24 final size:24
Alignment explanation
Indices: 271629--271678 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
271619 ATAAAGAACC
*
271629 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
271653 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
271677 AA
1 AA
271679 TCAACCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:274506 original size:19 final size:19
Alignment explanation
Indices: 274482--274523 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
274472 AAAACCAGAA
*
274482 CCCTAGGGGGTATCGATTC
1 CCCTAGGGGGAATCGATTC
*
274501 CCCTAGGGGGAATCGGTTC
1 CCCTAGGGGGAATCGATTC
274520 CCCT
1 CCCT
274524 TTAAAGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (19 bp):
CCCTAGGGGGAATCGATTC
Found at i:274535 original size:23 final size:22
Alignment explanation
Indices: 274505--274566 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
274495 CGATTCCCCT
274505 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGGTTCCCCTTT-A
* *
274528 AGGGGGAATCAGTTCACCTTTA
1 AGGGGGAATCGGTTCCCCTTTA
* *
274550 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
274567 TCTGCCCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.26
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTTA
Found at i:278419 original size:22 final size:21
Alignment explanation
Indices: 278377--278416 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
278367 TAAGTTTATT
*
278377 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
278398 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
278417 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:283919 original size:18 final size:19
Alignment explanation
Indices: 283896--283931 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
283886 GTAAACCTAG
283896 ATCAATACT-TGTGTATTA
1 ATCAATACTATGTGTATTA
283914 ATCAATACTATGTGTATT
1 ATCAATACTATGTGTATT
283932 TTATCCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (19 bp):
ATCAATACTATGTGTATTA
Found at i:289907 original size:77 final size:78
Alignment explanation
Indices: 289779--289932 Score: 215
Period size: 77 Copynumber: 2.0 Consensus size: 78
289769 ATATAGTAAG
* *
289779 TAAACATTAAAAGAATATATTCTGATTACAACTCTTTTAATTGATATTTAATTTGGAA-TAATTA
1 TAAACATTAAAAGAATATATTCGGATTACAACTCTTTTAATGGATATTTAATTT-GAATTAATTA
289843 AATAAGAGTTTAAA
65 AATAAGAGTTTAAA
** * *
289857 TAAACATTAAAGAGCGTA-ATTCGGATTATAAGTC-TTTAATGGATATTTAATTTGAATTAATTA
1 TAAACATTAAA-AGAATATATTCGGATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTA
289920 AATAAGAGTTTAA
65 AATAAGAGTTTAA
289933 TTAATTCGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
76 3 0.04
77 37 0.54
78 24 0.35
79 4 0.06
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.39
Consensus pattern (78 bp):
TAAACATTAAAAGAATATATTCGGATTACAACTCTTTTAATGGATATTTAATTTGAATTAATTAA
ATAAGAGTTTAAA
Found at i:290588 original size:16 final size:16
Alignment explanation
Indices: 290549--290615 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
290539 GACTGATACA
*
290549 AATTTGAACCAAAAAT
1 AATTTGAACCAAAAGT
** *
290565 AACATGAAGCAAAAGT
1 AATTTGAACCAAAAGT
*
290581 AATTTGAACCGAAAGT
1 AATTTGAACCAAAAGT
* **
290597 AACTTGAATAAAAAGT
1 AATTTGAACCAAAAGT
290613 AAT
1 AAT
290616 CTAAATCGAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (16 bp):
AATTTGAACCAAAAGT
Found at i:290590 original size:32 final size:32
Alignment explanation
Indices: 290549--290615 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
290539 GACTGATACA
*
290549 AATTTGAACCAAAAATAACATGAAGCAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
* * * *
290581 AATTTGAACCGAAAGTAACTTGAATAAAAAGT
1 AATTTGAACCAAAAATAACATGAAGAAAAAGT
290613 AAT
1 AAT
290616 CTAAATCGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.22
Consensus pattern (32 bp):
AATTTGAACCAAAAATAACATGAAGAAAAAGT
Found at i:290626 original size:32 final size:32
Alignment explanation
Indices: 290575--290646 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
290565 AACATGAAGC
* * * *
290575 AAAAGTAATTTGAACCGAAAGTAACTTGAATA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAACA
*
290607 AAAAGTAATCTAAATCGAAAGTAACCTGAACA
1 AAAAGTAATCTAAACCGAAAGTAACCTGAACA
290639 AAAAGTAA
1 AAAAGTAA
290647 CCTGACACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.54, C:0.11, G:0.14, T:0.21
Consensus pattern (32 bp):
AAAAGTAATCTAAACCGAAAGTAACCTGAACA
Found at i:290643 original size:16 final size:17
Alignment explanation
Indices: 290553--290651 Score: 57
Period size: 16 Copynumber: 6.2 Consensus size: 17
290543 GATACAAATT
*
290553 TGAACCAAAAA-TAACA
1 TGAACCAAAAAGTAACC
* **
290569 TGAAGC-AAAAGTAATT
1 TGAACCAAAAAGTAACC
* *
290585 TGAACC-GAAAGTAACT
1 TGAACCAAAAAGTAACC
* *
290601 TGAA-TAAAAAGTAATC
1 TGAACCAAAAAGTAACC
* * *
290617 TAAATC-GAAAGTAACC
1 TGAACCAAAAAGTAACC
290633 TGAA-CAAAAAGTAACC
1 TGAACCAAAAAGTAACC
290649 TGA
1 TGA
290652 CACATGTCAA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
15 5 0.08
16 58 0.92
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.19
Consensus pattern (17 bp):
TGAACCAAAAAGTAACC
Done.