Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012041.1 Corchorus olitorius cultivar O-4 contig12074, 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: 68130
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1231 original size:26 final size:26
Alignment explanation
Indices: 1202--1253 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1192 TTTTCTCAAA
*
1202 CTATTTTCTTAATCTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
** *
1228 CTATTTTATTGTTTTCTAGTTTAATT
1 CTATTTTATTAATCTCTAGTTTAATT
1254 TGCCTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (26 bp):
CTATTTTATTAATCTCTAGTTTAATT
Found at i:1980 original size:43 final size:43
Alignment explanation
Indices: 1915--2001 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
1905 TACATCAGAA
* *
1915 TTTTGTTAAAACTATGTTGTTTGTTTTTACTTTCTTCTTTTCG
1 TTTTGTTAAAACTATGTCGTTTGCTTTTACTTTCTTCTTTTCG
*
1958 TTTTGTTAGAACTATGTCGTTTGCTTTTACTTTCTTCTTTTCG
1 TTTTGTTAAAACTATGTCGTTTGCTTTTACTTTCTTCTTTTCG
2001 T
1 T
2002 CTTCTGTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.13, C:0.14, G:0.13, T:0.61
Consensus pattern (43 bp):
TTTTGTTAAAACTATGTCGTTTGCTTTTACTTTCTTCTTTTCG
Found at i:3727 original size:25 final size:25
Alignment explanation
Indices: 3671--3727 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
3661 CTTGAACATT
*
3671 CTTCTTATACTCTGACTTGATTATA
1 CTTCTTCTACTCTGACTTGATTATA
3696 CTTCTTCTACTCTGACTTGATTATA
1 CTTCTTCTACTCTGACTTGATTATA
3721 CTTCTTC
1 CTTCTTC
3728 ATATTTGAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.07, T:0.49
Consensus pattern (25 bp):
CTTCTTCTACTCTGACTTGATTATA
Found at i:4250 original size:39 final size:39
Alignment explanation
Indices: 4196--4304 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 39
4186 AGGATCTACT
*
4196 TAATAACGAAATCAAGG-GGACTGACGAAACATTGAAAGA
1 TAATAATGAAATCAAGGAGG-CTGACGAAACATTGAAAGA
* * *
4235 TAATAATGAAATCAAGGTGGTTGACGAAACATTGAAGGA
1 TAATAATGAAATCAAGGAGGCTGACGAAACATTGAAAGA
* * *
4274 TAATAATAAAAGCAAGGAGGCTGGCGAAACA
1 TAATAATGAAATCAAGGAGGCTGACGAAACA
4305 GTGGAGGAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 59 0.97
40 2 0.03
ACGTcount: A:0.47, C:0.11, G:0.25, T:0.17
Consensus pattern (39 bp):
TAATAATGAAATCAAGGAGGCTGACGAAACATTGAAAGA
Found at i:5151 original size:2 final size:2
Alignment explanation
Indices: 5144--5182 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5134 TTAGTGCCTT
5144 TA TA 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 TA TA T
5183 GATCAAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14028 original size:39 final size:39
Alignment explanation
Indices: 13975--14083 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 39
13965 AGGATCTACT
13975 TAATAATGAAATCAAGG-GGACTAACGAAACATTGAAAGA
1 TAATAATGAAATCAAGGAGG-CTAACGAAACATTGAAAGA
* * *
14014 TAATAATGAAATCAAGGAGGTTGACGAAACATTGAAGGA
1 TAATAATGAAATCAAGGAGGCTAACGAAACATTGAAAGA
* * **
14053 TAATAATAAAAGCAAGGAGGCTGGCGAAACA
1 TAATAATGAAATCAAGGAGGCTAACGAAACA
14084 GTGGAGGAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 60 0.97
40 2 0.03
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (39 bp):
TAATAATGAAATCAAGGAGGCTAACGAAACATTGAAAGA
Found at i:14583 original size:2 final size:2
Alignment explanation
Indices: 14576--14600 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14566 TCCGTCCCAT
14576 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 T
14601 TCTTGGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15256 original size:16 final size:17
Alignment explanation
Indices: 15224--15260 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
15214 AATCATTTAT
15224 TTATATAAATATAATAC
1 TTATATAAATATAATAC
*
15241 TTATATAAGT-TAATAC
1 TTATATAAATATAATAC
15257 TTAT
1 TTAT
15261 TATATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (17 bp):
TTATATAAATATAATAC
Found at i:23791 original size:23 final size:23
Alignment explanation
Indices: 23757--23805 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
23747 TTTTCCTCGT
*
23757 CATATCAGTATCAGATAAAGAGG
1 CATATCAATATCAGATAAAGAGG
23780 CATATCAATATCAGATAAAGAGG
1 CATATCAATATCAGATAAAGAGG
23803 CAT
1 CAT
23806 CAGAACCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (23 bp):
CATATCAATATCAGATAAAGAGG
Found at i:27779 original size:13 final size:12
Alignment explanation
Indices: 27742--27799 Score: 71
Period size: 13 Copynumber: 4.7 Consensus size: 12
27732 GATATTTTCG
**
27742 TTCCTAAAGGGA
1 TTCCTAAAGTCA
*
27754 TTGCTAAAGTCA
1 TTCCTAAAGTCA
27766 TTCCTAATAGTCA
1 TTCCTAA-AGTCA
27779 TTCCTAAAAGTCA
1 TTCCT-AAAGTCA
27792 TTCCTAAA
1 TTCCTAAA
27800 CCCCCAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
12 18 0.45
13 20 0.50
14 2 0.05
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (12 bp):
TTCCTAAAGTCA
Found at i:31689 original size:16 final size:16
Alignment explanation
Indices: 31668--31709 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
31658 TTACTCTGCT
31668 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
* *
31684 TTGTTTTC-ATTTTAA
1 TTGTTTTCTAGTATAA
31699 TTGTTATTCTA
1 TTGTT-TTCTA
31710 AACCCTCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 10 0.45
16 11 0.50
17 1 0.05
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:32110 original size:21 final size:22
Alignment explanation
Indices: 32071--32118 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
32061 TAATTTTGTG
32071 TTTTGCGTCAAAGAAAAAAAAA
1 TTTTGCGTCAAAGAAAAAAAAA
*
32093 TTTTGCGTCATA-AAAAAAAAA
1 TTTTGCGTCAAAGAAAAAAAAA
32114 TTTTG
1 TTTTG
32119 TCCCTGCGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (22 bp):
TTTTGCGTCAAAGAAAAAAAAA
Found at i:35265 original size:24 final size:21
Alignment explanation
Indices: 35210--35264 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
35200 CGCCCATTCA
*
35210 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCTAAGC
*
35231 CCGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCGGCTAAGC
*
35252 CCGTGCCATCACC
1 CCGTGCCACCACC
35265 ATTCCAAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (21 bp):
CCGTGCCACCACCGGCTAAGC
Found at i:43739 original size:24 final size:24
Alignment explanation
Indices: 43711--43777 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
43701 TAGGCCATTG
43711 GAGCAGCCACCACCTCCTCCAGAT
1 GAGCAGCCACCACCTCCTCCAGAT
** *
43735 GAGCAGCCAATACCTCCTCCAGTT
1 GAGCAGCCACCACCTCCTCCAGAT
*
43759 CAGCAGCCACCACCTCCTC
1 GAGCAGCCACCACCTCCTC
43778 TTGTCGAGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.24, C:0.46, G:0.15, T:0.15
Consensus pattern (24 bp):
GAGCAGCCACCACCTCCTCCAGAT
Found at i:50070 original size:50 final size:50
Alignment explanation
Indices: 50008--50292 Score: 455
Period size: 50 Copynumber: 5.6 Consensus size: 50
49998 CGATCAACTT
* * * *
50008 CTTTGAATTGTCTTCCAA-TCTAATATTAAAAGGATCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATC
*
50058 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCACTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
50108 CTTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAA-TCTTAAAAGGACCGTCTTCCGCTTATC
50159 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
50209 CTTTGAACTGTCTACCAATTCAATTCTATAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTACCAATTCAA-TCT-TAAAAGGACCGTCTTCCGCTTATC
*
50261 CTTTGAACTATCTACCAATTCAATCTTTAAAA
1 CTTTGAACTGTCTACCAATTCAATC-TTAAAA
50293 AAAGGTAATG
Statistics
Matches: 221, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
50 114 0.52
51 60 0.27
52 47 0.21
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:50182 original size:101 final size:102
Alignment explanation
Indices: 50034--50292 Score: 475
Period size: 101 Copynumber: 2.5 Consensus size: 102
50024 AATCTAATAT
*
50034 TAAAAGGATCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
50099 CCACTTATCCTTTGAACTGTCTACCAATTCAATTCTA
66 CCACTTATCCTTTGAACTGTCTACCAATTCAATTCTA
50136 -AAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
*
50200 CCGCTTATCCTTTGAACTGTCTACCAATTCAATTCTA
66 CCACTTATCCTTTGAACTGTCTACCAATTCAATTCTA
*
50237 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTATCTACCAATTCAATCTTTAAAA
1 TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC-TTAAAA
50293 AAAGGTAATG
Statistics
Matches: 152, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
101 99 0.65
102 47 0.31
103 6 0.04
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (102 bp):
TAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTT
CCACTTATCCTTTGAACTGTCTACCAATTCAATTCTA
Found at i:50419 original size:50 final size:50
Alignment explanation
Indices: 50343--50686 Score: 584
Period size: 50 Copynumber: 6.9 Consensus size: 50
50333 AAACCAAGGT
* * *
50343 TTGA-AAT-GACTCGTATGGAAAGGAGTTCGGCTTGTGGAAAAGCCTATG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
*
50391 TTGATAATCGACTCGTATGAAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
* * *
50441 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTAGAAAAGCCTATG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
50491 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
*
50541 TTGATAATCGACTCGTATGGAAACGAGCTTGGCTTGTGGAAAAGCCTGTG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
*
50591 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
*
50641 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC
50687 AAAACATTCA
Statistics
Matches: 280, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
48 4 0.01
49 3 0.01
50 273 0.98
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (50 bp):
TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
Found at i:51337 original size:50 final size:50
Alignment explanation
Indices: 51282--51480 Score: 254
Period size: 50 Copynumber: 4.0 Consensus size: 50
51272 CTTAAATGCC
* * *
51282 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * * *
51332 CTTTGAAAAGCGAATTTTAATCTCGAACTCACAGATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * * * *
51382 TTTTGAAAAGTGAATTTTGATCTTGAACCCTCAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * * *
51432 TTTTGAACAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATCTT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTT
51481 GTTATAGAAC
Statistics
Matches: 128, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 128 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:53869 original size:29 final size:28
Alignment explanation
Indices: 53837--53908 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
53827 CAAACAACCC
* *
53837 AAATGCCCCTGGATATGTAGAAATGATCA
1 AAATACCCCTGAATATGTAGAAATGA-CA
53866 AAATACCCCTGAATATGTAGAAATGACA
1 AAATACCCCTGAATATGTAGAAATGACA
*
53894 AAAGTACCCATGAAT
1 AAA-TACCCCTGAAT
53909 GTGTTAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (28 bp):
AAATACCCCTGAATATGTAGAAATGACA
Found at i:54089 original size:15 final size:16
Alignment explanation
Indices: 54069--54102 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
54059 TGAAAGATAG
*
54069 CAATTAAAC-AGAAAA
1 CAATTAAACTACAAAA
54084 CAATTAAACTACAAAA
1 CAATTAAACTACAAAA
54100 CAA
1 CAA
54103 AACAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.18, G:0.03, T:0.15
Consensus pattern (16 bp):
CAATTAAACTACAAAA
Found at i:54897 original size:17 final size:18
Alignment explanation
Indices: 54860--54897 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54850 ACCCTTGTCT
*
54860 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACGA
*
54878 AAAACTAGAGGAAAA-GA
1 AAAACTAGAAGAAAACGA
54895 AAA
1 AAA
54898 TATCTATGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (18 bp):
AAAACTAGAAGAAAACGA
Found at i:56588 original size:31 final size:31
Alignment explanation
Indices: 56550--56610 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
56540 TATTTTGACA
56550 TATTGTAAATTTAAATTTACAAACCTTGAAG
1 TATTGTAAATTTAAATTTACAAACCTTGAAG
*
56581 TATTGTAAATTTTAATTTACAAACCTTGAA
1 TATTGTAAATTTAAATTTACAAACCTTGAA
56611 TTTTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTGTAAATTTAAATTTACAAACCTTGAAG
Found at i:64075 original size:36 final size:36
Alignment explanation
Indices: 64028--64097 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
64018 TTCAATAACC
* **
64028 TTACATATTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATATTTTGTAATTTTAATTATCATATTTCTTA
*
64064 TTACATTTTTTGTAATTTTAATTATCATATTTCT
1 TTACATATTTTGTAATTTTAATTATCATATTTCT
64098 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATATTTTGTAATTTTAATTATCATATTTCTTA
Found at i:65070 original size:207 final size:202
Alignment explanation
Indices: 64609--65224 Score: 1072
Period size: 202 Copynumber: 3.0 Consensus size: 202
64599 GCTTAATAAC
* *
64609 TTTATTAATTGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTA-AATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAG-AGAATA
* *
64673 AGATACAACACATTATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
65 AGATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTT
* *
64738 GAATTATTAAATTAAATTAAATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
130 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
64803 CCGATTTA
195 CCGATTTA
64811 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGAGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGAGAATAA
*
64876 GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTATTGGTTG
66 GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
64941 ATTTATTAAATTAAATTAGATCTTTTCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
131 ATTTATTAAATTAAATTAGA-----TCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
*
65006 AGATCCTATTTA
191 AGATCCGATTTA
* *
65018 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGAGAATAA
*
65083 GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACTTTAGTGGTTG
66 GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
65148 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
65213 CGATTTA
196 CGATTTA
65220 TTTAT
1 TTTAT
65225 TATTAAGGAA
Statistics
Matches: 395, Mismatches: 13, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
201 1 0.00
202 197 0.50
207 197 0.50
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (202 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGAGAATAA
GATACAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
CGATTTA
Found at i:65402 original size:41 final size:40
Alignment explanation
Indices: 65336--65416 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
65326 CCTAAAAATT
*
65336 TAATTAATATAAGTATTTCAATTATTATA-GTATTACATA
1 TAATTAATATAAGTATTTCAATTATTATATATATTACATA
* *
65375 TAATTAATATGTAAGTATTTTAGTTATTATATATATTACATA
1 TAATTAATA--TAAGTATTTCAATTATTATATATATTACATA
65417 GGAATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 9 0.25
41 18 0.50
42 9 0.25
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (40 bp):
TAATTAATATAAGTATTTCAATTATTATATATATTACATA
Found at i:65642 original size:2 final size:2
Alignment explanation
Indices: 65631--65665 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
65621 AGTTTAGACT
65631 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65666 AGAGAATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.