Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015297.1 Corchorus olitorius cultivar O-4 contig15330, 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: 39440
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1137 original size:38 final size:38
Alignment explanation
Indices: 1050--1634 Score: 784
Period size: 39 Copynumber: 15.1 Consensus size: 38
1040 CTAAAAGATA
* *
1050 AAAGATGACCTGTTTCTAGTCAACTTTGATAAATACTTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
* * *
1089 AAACATGACCTGTTTCCAGTCAACTTTCATAACTATTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
* *
1127 AAAGATGACCTGTTTCAAGTCAACTTTGATAAATACTTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
*
1166 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTGCTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
*
1204 AAAAGATGACCTGTTTCCAGTCAACTTTGATAACCACTTG
1 -AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
* * *
1244 AAATATGACCTGTTGCCAGTCAACTTTGATAACTACGG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
* *
1282 AAAGATGACCTGTTTCCAGTCAA-TCTTGATAACTGCTA
1 AAAGATGACCTGTTTCCAGTCAACT-TTGATAACTACTG
*
1320 AAAGATGACCTGTTTCCAGTTCCAGTCAACTTTGATAAATACTTG
1 AAAGATGACCTG--T----TTCCAGTCAACTTTGATAACTAC-TG
1365 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
*
1403 AAAGATGACCTGTTTCCAATCAACTTTGATAACTACTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
*
1441 AAAGATGACCTGTTTCCAGTCAACTTTGATAACCACTTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
* * *
1480 AAAGATGACCTGTTTCCAGCCAACTTTGATAACTGCGG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
* *
1518 AAAGATGACCTGTTTCTAGTCAA-TCTTGATAACTGCTG
1 AAAGATGACCTGTTTCCAGTCAACT-TTGATAACTACTG
1556 AAAAGATGACCTGTTTCC-GATCAACTTTGAT-A-TACTG
1 -AAAGATGACCTGTTTCCAG-TCAACTTTGATAACTACTG
1593 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTG
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TG
1632 AAA
1 AAA
1635 ATTTTTTGAA
Statistics
Matches: 485, Mismatches: 40, Indels: 42
0.86 0.07 0.07
Matches are distributed among these distances:
36 28 0.06
37 8 0.02
38 191 0.39
39 220 0.45
40 4 0.01
43 1 0.00
44 19 0.04
45 14 0.03
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (38 bp):
AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTG
Found at i:1148 original size:77 final size:77
Alignment explanation
Indices: 1050--1634 Score: 808
Period size: 77 Copynumber: 7.5 Consensus size: 77
1040 CTAAAAGATA
* * *
1050 AAAGATGACCTGTTTCTAGTCAACTTTGATAAATACTTGAAACATGACCTGTTTCCAGTCAACTT
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAACTT
* *
1115 TCATAACTATTG
66 TGATAACTACTG
* *
1127 AAAGATGACCTGTTTCAAGTCAACTTTGATAAATACTTGAAAGATGACCTGTTTCCAGTCAACTT
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAACTT
*
1192 TGATAACTGCTG
66 TGATAACTACTG
* * *
1204 AAAAGATGACCTGTTTCCAGTCAACTTTGATAACCACTTGAAATATGACCTGTTGCCAGTCAACT
1 -AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAACT
*
1269 TTGATAACTACGG
65 TTGATAACTACTG
* *
1282 AAAGATGACCTGTTTCCAGTCAA-TCTTGATAACTGC-TAAAAGATGACCTGTTTCCAGTTCCAG
1 AAAGATGACCTGTTTCCAGTCAACT-TTGATAACTACTTGAAAGATGACCTG--T----TTCCAG
*
1345 TCAACTTTGATAAATACTTG
59 TCAACTTTGATAACTAC-TG
*
1365 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTAC-TGAAAGATGACCTGTTTCCAATCAACTT
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAACTT
1429 TGATAACTACTG
66 TGATAACTACTG
* *
1441 AAAGATGACCTGTTTCCAGTCAACTTTGATAACCACTTGAAAGATGACCTGTTTCCAGCCAACTT
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAACTT
* *
1506 TGATAACTGCGG
66 TGATAACTACTG
* *
1518 AAAGATGACCTGTTTCTAGTCAA-TCTTGATAACTGC-TGAAAAGATGACCTGTTTCC-GATCAA
1 AAAGATGACCTGTTTCCAGTCAACT-TTGATAACTACTTG-AAAGATGACCTGTTTCCAG-TCAA
1580 CTTTGAT-A-TACTG
63 CTTTGATAACTACTG
1593 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAA
1 AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAA
1635 ATTTTTTGAA
Statistics
Matches: 456, Mismatches: 36, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
75 38 0.08
76 58 0.13
77 219 0.48
78 71 0.16
81 1 0.00
82 21 0.05
83 47 0.10
84 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (77 bp):
AAAGATGACCTGTTTCCAGTCAACTTTGATAACTACTTGAAAGATGACCTGTTTCCAGTCAACTT
TGATAACTACTG
Found at i:1720 original size:54 final size:54
Alignment explanation
Indices: 1650--1904 Score: 290
Period size: 54 Copynumber: 4.8 Consensus size: 54
1640 TTGAACGATT
*
1650 GCACTAGATCACTTGAAGATAAACTTAAACCACTAG-AAACTTTCTTGATTGTCC
1 GCACTAGATCACTTGAAGATAAACTTAAACCACT-GTAAACTTTCTTGATTGACC
*
1704 GCACTAGATCGA-TTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACT
1 GCACTAGATC-ACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACC
* * * * **
1758 GCACTGGATCACTTTAAGATAAACTTGAACCACTGTAATCTTTC-TGACCGACC
1 GCACTAGATCACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACC
* * * *
1811 GCACTGGATCTTCTTGAAAATAAACTTAAACCACTGTAAA----CTTGATTGATC
1 GCACTAGATC-ACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACC
* * *
1862 GCACTGGATCCCTTTGAAGATAAACTCAAACCACTGTAAACTT
1 GCACTAGATCAC-TTGAAGATAAACTTAAACCACTGTAAACTT
1905 GATTGATCAC
Statistics
Matches: 172, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.01
51 41 0.24
53 18 0.10
54 110 0.64
55 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29
Consensus pattern (54 bp):
GCACTAGATCACTTGAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACC
Found at i:2019 original size:24 final size:24
Alignment explanation
Indices: 1968--2039 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
1958 ACTGGATCAT
* * *
1968 TTGAAGTAATTTGAAGCATTGTAGAA
1 TTGAAG-AATTGGAA-CATTGAATAA
1994 TTGAAGAATTGGAACATTGAATAA
1 TTGAAGAATTGGAACATTGAATAA
* *
2018 TTGAA-AAATGGAGCATTGAATA
1 TTGAAGAATTGGAACATTGAATA
2040 CCCCTAATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 15 0.37
24 13 0.32
25 7 0.17
26 6 0.15
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (24 bp):
TTGAAGAATTGGAACATTGAATAA
Found at i:2105 original size:26 final size:25
Alignment explanation
Indices: 2063--2118 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
2053 TGAAATACAG
* *
2063 TGAAGAAAGACCACCCTGGGTCATTT
1 TGAAGAAAGACCACCCTAGATCA-TT
* *
2089 TGAAGAAAGATCGCCCTAGATCATT
1 TGAAGAAAGACCACCCTAGATCATT
2114 TGAAG
1 TGAAG
2119 TAAACTGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
TGAAGAAAGACCACCCTAGATCATT
Found at i:2425 original size:106 final size:105
Alignment explanation
Indices: 2089--2700 Score: 617
Period size: 106 Copynumber: 5.8 Consensus size: 105
2079 TGGGTCATTT
* * * ** * * * * *
2089 TGAAGAAAGATCGCCCTAGATCATTTGAAGTAAACTGAAGAATGATCGCCTTGGATCAATTGAAA
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAA
* * * *
2154 TTAACCGAAGAAAGATCGCCCTGGATCAATTGAAGTAAA-
66 TAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAAC
* * * * *
2193 TCGAAGAAAGACCGCCCTGGGTGAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGA
1 T-GAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCA-ACTGA
* * * *
2258 CATAAACTGAAGACACATCGCCCTGG-GCAACTGAAATAAAC
64 AATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAAC
* * * * * *
2299 TAAAGAAAGACCGCCCTGGGTTAACCGAAATAAACTGAAGAATGATCGCCCTGGATTAACTGAAA
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAA
* * *
2364 TAAACTGAAGAAAAGACCACCCTGGGTCAACTGAAATAAAC
66 TAAACTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAAC
* * * *
2405 TGAAGAAAGACCGTCGTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTAGG-TTAATTGAA
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCT-GGATCAACTGAA
* *
2469 ATAAACTGAAGAATA-ATCGCCCTAGATCAACTTGAAGA-CAAC
65 ATAAACTGAAGAA-AGATCGCCCTGGATCAAC-TGAA-ATAAAC
* ** * *
2511 TGAAGAAAGACCACCCCAGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTTAACTGAAA
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAA
* * *
2576 TAAACTGAAGAATGATCGCCTTGGATCAACTTGAAGACAAA-
66 TAAACTGAAGAAAGATCGCCCTGGATCAAC-TGAA-ATAAAC
* * * * *
2617 TGAAGAAAGACCACCC-CGGTCAACTGAAATGAACTGAAGAAAGACCGCCATGGGTCAACTGAAA
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAA
* *
2681 CAAACTGAAGAAAGACCGCC
66 TAAACTGAAGAAAGATCGCC
2701 TTAAGTCAAC
Statistics
Matches: 429, Mismatches: 67, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
104 16 0.04
105 192 0.45
106 216 0.50
107 5 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (105 bp):
TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGATCAACTGAAA
TAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAAAC
Found at i:2470 original size:141 final size:139
Alignment explanation
Indices: 2114--2700 Score: 617
Period size: 141 Copynumber: 4.2 Consensus size: 139
2104 CTAGATCATT
* * * * * * * * *
2114 TGAAGTAAACTGAAGAATGATCGCCTTGGATCAATTGAAATTAACCGAAGAAAGATCGCCCTGGA
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* * * *
2179 TCAATTGAAGTAAATCGAAGAAAGACCGCCCTGGGTGAACTGAAATAAACTGAAGAACGACCACC
66 TCAATTGAAATAAAT-GAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCACC
* * *
2244 CTCGATCATTC
130 CTGGGTCA-AC
* * * * * *
2255 TGACATAAACTGAAGACACATCGCCCTGGG-CAACTGAAATAAACTAAAGAAAGACCGCCCTGGG
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* ** * * *
2319 TTAACCGAAATAAACTGAAGAATGATCGCCCTGGATTAACTGAAATAAACTGAAGAAAAGACCAC
66 TCAATTGAAATAAA-TGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGACCAC
2384 CCTGGGTCAAC
129 CCTGGGTCAAC
* *
2395 TGAAATAAACTGAAGAAAGACCGTCGTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTAGG
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCT-GG
* * * *
2460 -TTAATTGAAATAAACTGAAGAATA-ATCGCCCTAGATCAACTTGAAGA-CAACTGAAGAAAGAC
65 ATCAATTGAAATAAA-TGAAGAA-AGACCGCCCTGGATCAAC-TGAA-ATAAACTGAAGAAAGAC
**
2522 CACCCCAGGTCAAC
126 CACCCTGGGTCAAC
* * * *
2536 TGAAATAAACTGAAGAAAGACCGCCCTGGGTTAACTGAAATAAACTGAAGAATGATCGCCTTGGA
1 TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
* * * * *
2601 TCAACTTGAAGACAAATGAAGAAAGACCACCCCGG-TCAACTGAAATGAACTGAAGAAAGACCGC
66 TCAA-TTGAA-ATAAATGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCAC
*
2665 CATGGGTCAAC
129 CCTGGGTCAAC
*
2676 TGAAACAAACTGAAGAAAGACCGCC
1 TGAAATAAACTGAAGAAAGACCGCC
2701 TTAAGTCAAC
Statistics
Matches: 376, Mismatches: 58, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
139 1 0.00
140 152 0.40
141 186 0.49
142 32 0.09
143 5 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (139 bp):
TGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
TCAATTGAAATAAATGAAGAAAGACCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCACCC
TGGGTCAAC
Found at i:2711 original size:35 final size:35
Alignment explanation
Indices: 2089--2700 Score: 588
Period size: 35 Copynumber: 17.4 Consensus size: 35
2079 TGGGTCATTT
* * * ** *
2089 TGAAGAAAGATCGCCCTAGATCATTTGAAGTAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * * * * *
2124 TGAAGAATGATCGCCTTGGATCAATTGAAATTAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * * * *
2159 CGAAGAAAGATCGCCCTGGATCAATTGAAGTAAA-
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
*
2193 TCGAAGAAAGACCGCCCTGGGTGAACTGAAATAAAC
1 T-GAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * * * * *
2229 TGAAGAACGACCACCCTCGATCATTCTGACATAAAC
1 TGAAGAAAGACCGCCCTGGGTCA-ACTGAAATAAAC
* * *
2265 TGAAGACACATCGCCCTGGG-CAACTGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * *
2299 TAAAGAAAGACCGCCCTGGGTTAACCGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * * *
2334 TGAAGAATGATCGCCCTGGATTAACTGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
*
2369 TGAAGAAAAGACCACCCTGGGTCAACTGAAATAAAC
1 TGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAAC
* *
2405 TGAAGAAAGACCGTCGTGGGTCAACTGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * *
2440 TGAAGAAAGACCGCCCTAGGTTAATTGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * * *
2475 TGAAGAATA-ATCGCCCTAGATCAACTTGAAGA-CAAC
1 TGAAGAA-AGACCGCCCTGGGTCAAC-TGAA-ATAAAC
* **
2511 TGAAGAAAGACCACCCCAGGTCAACTGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
*
2546 TGAAGAAAGACCGCCCTGGGTTAACTGAAATAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* * * * *
2581 TGAAGAATGATCGCCTTGGATCAACTTGAAGACAAA-
1 TGAAGAAAGACCGCCCTGGGTCAAC-TGAA-ATAAAC
* * *
2617 TGAAGAAAGACCACCC-CGGTCAACTGAAATGAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
* *
2651 TGAAGAAAGACCGCCATGGGTCAACTGAAACAAAC
1 TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
2686 TGAAGAAAGACCGCC
1 TGAAGAAAGACCGCC
2701 TTAAGTCAAC
Statistics
Matches: 473, Mismatches: 90, Indels: 28
0.80 0.15 0.05
Matches are distributed among these distances:
33 3 0.01
34 45 0.10
35 323 0.68
36 97 0.21
37 5 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (35 bp):
TGAAGAAAGACCGCCCTGGGTCAACTGAAATAAAC
Found at i:3794 original size:6 final size:6
Alignment explanation
Indices: 3785--3848 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
3775 GAACTTTATC
*
3785 TTTTCT TTTTCCTT TTGTTCT TTTTCT TTTTCT TTTTC- TTTT-T TTCTCT
1 TTTTCT TTTT-C-T TT-TTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* *
3834 TTTTTT TTTTAT TTT
1 TTTTCT TTTTCT TTT
3849 ACTTCACTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
5 7 0.14
6 32 0.65
7 4 0.08
8 4 0.08
9 2 0.04
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:3807 original size:15 final size:13
Alignment explanation
Indices: 3785--3848 Score: 67
Period size: 14 Copynumber: 4.7 Consensus size: 13
3775 GAACTTTATC
3785 TTTTCTTTTTCCTT
1 TTTTCTTTTT-CTT
3799 TTGTTCTTTTTC-T
1 TT-TTCTTTTTCTT
3812 TTTTCTTTTTCTTT
1 TTTTCTTTTTC-TT
*
3826 TTTTCTCTTTTTTT
1 TTTTCT-TTTTCTT
*
3840 TTTTATTTT
1 TTTTCTTTT
3849 ACTTCACTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 9 0.20
13 6 0.14
14 17 0.39
15 12 0.27
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:3807 original size:26 final size:26
Alignment explanation
Indices: 3778--3831 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3768 CACCCAAGAA
3778 CTTTATC-TTTTCTTTTTCCTTTTGTT
1 CTTTATCTTTTTCTTTTT-CTTTTGTT
* *
3804 CTTTTTCTTTTTCTTTTTCTTTTTTT
1 CTTTATCTTTTTCTTTTTCTTTTGTT
3830 CT
1 CT
3832 CTTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (26 bp):
CTTTATCTTTTTCTTTTTCTTTTGTT
Found at i:3809 original size:21 final size:21
Alignment explanation
Indices: 3785--3837 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3775 GAACTTTATC
*
3785 TTTTCTTTTTCCTTTTGTTCT
1 TTTTCTTTTTCCTTTTCTTCT
* *
3806 TTTTCTTTTTCTTTTTCTTTT
1 TTTTCTTTTTCCTTTTCTTCT
3827 TTTCTCTTTTT
1 TTT-TCTTTTT
3838 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTCTTTTTCCTTTTCTTCT
Found at i:3815 original size:27 final size:28
Alignment explanation
Indices: 3785--3848 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
3775 GAACTTTATC
3785 TTTTCTTTTTCCTTTTGT-TCTTTTTCT
1 TTTTCTTTTTCCTTTTGTCTCTTTTTCT
* * *
3812 TTTTCTTTTTCTTTTTTTCTCTTTTTTT
1 TTTTCTTTTTCCTTTTGTCTCTTTTTCT
*
3840 TTTTATTTT
1 TTTTCTTTT
3849 ACTTCACTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (28 bp):
TTTTCTTTTTCCTTTTGTCTCTTTTTCT
Found at i:3933 original size:22 final size:21
Alignment explanation
Indices: 3906--3952 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3896 CTAAAAACCT
* *
3906 TTTTGAGAAAAACATTTTTTTC
1 TTTTGA-AAAAACAATTTCTTC
*
3928 TTTTGAAAAATCAATTTCTTC
1 TTTTGAAAAAACAATTTCTTC
3949 TTTT
1 TTTT
3953 TGAACAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTGAAAAAACAATTTCTTC
Found at i:3953 original size:22 final size:22
Alignment explanation
Indices: 3904--3961 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3894 CTCTAAAAAC
* * *
3904 CTTTTTGAGAAAAACATTTTTTT
1 CTTTTTGA-AAAATCAATTTCTT
3927 C-TTTTGAAAAATCAATTTCTT
1 CTTTTTGAAAAATCAATTTCTT
*
3948 CTTTTTGAACAATC
1 CTTTTTGAAAAATC
3962 CTTTCACCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 12 0.40
22 17 0.57
23 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (22 bp):
CTTTTTGAAAAATCAATTTCTT
Found at i:4561 original size:14 final size:13
Alignment explanation
Indices: 4525--4575 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
4515 CTCAAAAATC
4525 TTTTGAAAACTCATT
1 TTTTGAAAAC-C-TT
4540 TTTT-AAAACCTT
1 TTTTGAAAACCTT
*
4552 TTCTTGAAAACATAT
1 TT-TTGAAAACCT-T
4567 TTTTGAAAA
1 TTTTGAAAA
4576 ACCTCTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 18 0.56
15 7 0.22
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTGAAAACCTT
Found at i:7447 original size:52 final size:52
Alignment explanation
Indices: 7349--7638 Score: 458
Period size: 52 Copynumber: 5.6 Consensus size: 52
7339 ACTGAAACCG
* * *
7349 AAACTGACGGGAACTTTCCCTAAATTGAAAACCG-GCTAAATTGAATACTTTGA
1 AAACTGATGGGAACTTTCCC-AATTTG-AAACAGAGCTAAATTGAATACTTTGA
7402 AAACTGATGGGAACTTTCCCAATTTGAAACAGAGCTAAATTGAATACTTTGA
1 AAACTGATGGGAACTTTCCCAATTTGAAACAGAGCTAAATTGAATACTTTGA
*
7454 AAACTGGTGGGAACTTTCCCAATTTGAAA-AGGAGCTAAATTGAATACTTTGA
1 AAACTGATGGGAACTTTCCCAATTTGAAACA-GAGCTAAATTGAATACTTTGA
* *
7506 AAACTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGA
1 AAACTGATGGGAACTTTCCCAATTTGAAACAGAGCTAAATTGAATACTTTGA
*
7558 AGACTGATGGGAACTTTCCCAATTTGAAACAGAGCTAAATTGAATACTTTGA
1 AAACTGATGGGAACTTTCCCAATTTGAAACAGAGCTAAATTGAATACTTTGA
* *
7610 AGACTGATGGGAAGTTTCCCAATTTGAAA
1 AAACTGATGGGAACTTTCCCAATTTGAAA
7639 ATTTAAAAAC
Statistics
Matches: 226, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
51 6 0.03
52 200 0.88
53 20 0.09
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (52 bp):
AAACTGATGGGAACTTTCCCAATTTGAAACAGAGCTAAATTGAATACTTTGA
Found at i:7480 original size:27 final size:27
Alignment explanation
Indices: 7449--7535 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
7439 AATTGAATAC
7449 TTTGAAAACTGGTGGGAACTTTCCCAA
1 TTTGAAAACTGGTGGGAACTTTCCCAA
* ** * **** *
7476 TTTGAAAA--GGAGCTAAATTGAATAC
1 TTTGAAAACTGGTGGGAACTTTCCCAA
7501 TTTGAAAACTGGTGGGAACTTTCCCAA
1 TTTGAAAACTGGTGGGAACTTTCCCAA
7528 TTTGAAAA
1 TTTGAAAA
7536 AGAGCTAAAT
Statistics
Matches: 40, Mismatches: 18, Indels: 4
0.65 0.29 0.06
Matches are distributed among these distances:
25 16 0.40
27 24 0.60
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (27 bp):
TTTGAAAACTGGTGGGAACTTTCCCAA
Found at i:7637 original size:36 final size:36
Alignment explanation
Indices: 7597--7751 Score: 170
Period size: 36 Copynumber: 4.2 Consensus size: 36
7587 CAGAGCTAAA
* * *
7597 TTGAATACTTTGAAGAC-TGATGGGAAGTTTCCCAAT
1 TTGAA-ACTTTAAAAACTTGATGGGAACTTTCCCAAT
* *
7633 TTGAAAATTTAAAAACTTGGTGGGAACTTTCCCAAT
1 TTGAAACTTTAAAAACTTGATGGGAACTTTCCCAAT
* *
7669 TTGAAAAC-TTAAAAACTTGGTGGGAACTTTCCCGAT
1 TTG-AAACTTTAAAAACTTGATGGGAACTTTCCCAAT
* * *
7705 TTGAAAATTTGGAAAACTGGATGGGAACTTTCCCAAT
1 TTGAAACTTT-AAAAACTTGATGGGAACTTTCCCAAT
7742 TTGAAGACTT
1 TTGAA-ACTT
7752 AAACCTGATG
Statistics
Matches: 101, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
35 11 0.11
36 57 0.56
37 30 0.30
38 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (36 bp):
TTGAAACTTTAAAAACTTGATGGGAACTTTCCCAAT
Found at i:7730 original size:37 final size:36
Alignment explanation
Indices: 7617--7746 Score: 199
Period size: 36 Copynumber: 3.6 Consensus size: 36
7607 TGAAGACTGA
*
7617 TGGGAAGTTTCCCAATTTGAAAATTTAAAAACTTGG
1 TGGGAACTTTCCCAATTTGAAAATTTAAAAACTTGG
*
7653 TGGGAACTTTCCCAATTTGAAAACTTAAAAACTTGG
1 TGGGAACTTTCCCAATTTGAAAATTTAAAAACTTGG
* *
7689 TGGGAACTTTCCCGATTTGAAAATTTGGAAAAC-TGG
1 TGGGAACTTTCCCAATTTGAAAATTT-AAAAACTTGG
7725 ATGGGAACTTTCCCAATTTGAA
1 -TGGGAACTTTCCCAATTTGAA
7747 GACTTAAACC
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
36 61 0.71
37 25 0.29
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (36 bp):
TGGGAACTTTCCCAATTTGAAAATTTAAAAACTTGG
Found at i:7745 original size:73 final size:72
Alignment explanation
Indices: 7617--7754 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 72
7607 TGAAGACTGA
*
7617 TGGGAAGTTTCCCAATTTGAAAATTTAAAAACTTGGTGGGAACTTTCCCAATTTGAAAACTTAAA
1 TGGGAACTTTCCCAATTTGAAAATTTAAAAACTTGGTGGGAACTTTCCCAATTTGAAAACTTAAA
7682 AACTTGG
66 AACTTGG
* * *
7689 TGGGAACTTTCCCGATTTGAAAATTTGGAAAAC-TGGATGGGAACTTTCCCAATTTGAAGACTTA
1 TGGGAACTTTCCCAATTTGAAAATTT-AAAAACTTGG-TGGGAACTTTCCCAATTTGAAAACTTA
7753 AA
64 AA
7755 CCTGATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 27 0.45
73 33 0.55
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (72 bp):
TGGGAACTTTCCCAATTTGAAAATTTAAAAACTTGGTGGGAACTTTCCCAATTTGAAAACTTAAA
AACTTGG
Found at i:21655 original size:34 final size:32
Alignment explanation
Indices: 21612--21687 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
21602 GTTGCCTTGT
21612 GCGCGGGCTGGACAGGCAGCAGCCCCGTGCTGGC
1 GCGCGGGCTGGACAGGC--CAGCCCCGTGCTGGC
* * ** *
21646 GCGCGGGCTGGCCTGGCTTGTCCCGTGCTGGC
1 GCGCGGGCTGGACAGGCCAGCCCCGTGCTGGC
21678 GCGCGGGCTG
1 GCGCGGGCTG
21688 TGCGGTGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 22 0.59
34 15 0.41
ACGTcount: A:0.05, C:0.34, G:0.46, T:0.14
Consensus pattern (32 bp):
GCGCGGGCTGGACAGGCCAGCCCCGTGCTGGC
Found at i:30761 original size:32 final size:32
Alignment explanation
Indices: 30699--30849 Score: 143
Period size: 32 Copynumber: 4.8 Consensus size: 32
30689 TTCCTATAAA
* *
30699 AAAACCCCTA-ATTT-GGGGCGTCCATAGAAG
1 AAAACCCCTATATTTAGGGGCGTCTATTGAAG
**
30729 AAAACCCCTATATTTAGCAGCGTCTATTGAAG
1 AAAACCCCTATATTTAGGGGCGTCTATTGAAG
* **
30761 AAAACGCCT-TAAAATAGGGGCGTCTATTGAAG
1 AAAACCCCTAT-ATTTAGGGGCGTCTATTGAAG
* *
30793 AAAACGCCC-CTATTTAGGGGTGTCTATTGAAG
1 AAAAC-CCCTATATTTAGGGGCGTCTATTGAAG
*
30825 AAAACACCC-CTATTTA-GGGCGTCTA
1 AAAAC-CCCTATATTTAGGGGCGTCTA
30850 CAAGGAAAAC
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
30 10 0.10
31 13 0.13
32 75 0.74
33 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (32 bp):
AAAACCCCTATATTTAGGGGCGTCTATTGAAG
Found at i:30843 original size:64 final size:65
Alignment explanation
Indices: 30697--30849 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 65
30687 TTTTCCTATA
* *
30697 AAAAAACCCCTAATTT-GGGGCGTCCATAGAAGAAAACCCCTATATTTAGCAGCGTCTATTGAAG
1 AAAACACCCCTAATTTAGGGGCGTCTATAGAAGAAAACCCCTATATTTAGCAGCGTCTATTGAAG
* * ** * * ** *
30761 AAAAC-GCCTTAAAATAGGGGCGTCTATTGAAGAAAACGCCC-CTATTTAGGGGTGTCTATTGAA
1 AAAACACCCCTAATTTAGGGGCGTCTATAGAAGAAAAC-CCCTATATTTAGCAGCGTCTATTGAA
30824 G
65 G
30825 AAAACACCCCT-ATTTA-GGGCGTCTA
1 AAAACACCCCTAATTTAGGGGCGTCTA
30850 CAAGGAAAAC
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
63 15 0.21
64 50 0.70
65 6 0.08
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (65 bp):
AAAACACCCCTAATTTAGGGGCGTCTATAGAAGAAAACCCCTATATTTAGCAGCGTCTATTGAAG
Found at i:32910 original size:44 final size:44
Alignment explanation
Indices: 32852--32939 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
32842 AAAATTAGTA
* *
32852 AATCGAGTATTGAAGATTGGTTTTAGCGTTCGAGTACAAAAATG
1 AATCAAGTATTGAAGATTGGTTTTAACGTTCGAGTACAAAAATG
* * *
32896 AATCAAGTTTTGAAGATTGGTTTTAACGTTGGGGTACAAAAATG
1 AATCAAGTATTGAAGATTGGTTTTAACGTTCGAGTACAAAAATG
32940 GGTTGAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (44 bp):
AATCAAGTATTGAAGATTGGTTTTAACGTTCGAGTACAAAAATG
Found at i:34158 original size:60 final size:60
Alignment explanation
Indices: 34021--34180 Score: 259
Period size: 60 Copynumber: 2.7 Consensus size: 60
34011 TCGATGCTAG
* **
34021 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTA-TTGGCCAAATTAAAAAATCGG
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTCGCCAAATTAAAAAATCAA
* *
34080 GCCCTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTCGCCAAATTAAAAGATCAA
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTCGCCAAATTAAAAAATCAA
*
34140 GCCTTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
1 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTT
34181 GAGCAATTAG
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 37 0.40
60 56 0.60
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTCGCCAAATTAAAAAATCAA
Found at i:37454 original size:31 final size:31
Alignment explanation
Indices: 37402--37602 Score: 287
Period size: 31 Copynumber: 6.5 Consensus size: 31
37392 TCCTTTTGTG
* * *
37402 CACGTAGCATGCCACGTGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
* * **
37433 CACATAGCGTGATACGA-GTCACTTTTTGGTA
1 CACGTGGCGTGCCAC-ATGTCACTTTTTGGTA
*
37464 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
*
37495 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
*
37526 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
37557 CACGTGGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCGTGCCACATGTCACTTTTTGGTA
*
37588 CACGTGGCATGCCAC
1 CACGTGGCGTGCCAC
37603 GTCGGACACC
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
30 1 0.01
31 155 0.99
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (31 bp):
CACGTGGCGTGCCACATGTCACTTTTTGGTA
Done.