Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020316.1 Corchorus olitorius cultivar O-4 contig20349, 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: 83059
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:2082 original size:33 final size:33
Alignment explanation
Indices: 2012--2174 Score: 116
Period size: 33 Copynumber: 4.9 Consensus size: 33
2002 ATGATCAACC
** *
2012 AAAACAGATTT-GTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTAG-TTTCATCACAAACAACA-CCT
2045 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT
** * *
2078 AAAACAGATTTAGAGTCATCATAAACAACACTT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
2111 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
* * * **
2144 AAAACATATTTCGTGTCATTGCAAACAACAC
1 AAAACAGATTTAGTTTCATCACAAACAACAC
2175 TCAAATTAGG
Statistics
Matches: 101, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
32 6 0.06
33 90 0.89
34 5 0.05
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:2130 original size:66 final size:66
Alignment explanation
Indices: 2060--2186 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
2050 AGAATTTGTT
* *
2060 TCATCACAAACAACACCTAAAACAGATTTAGAGTCATCATAAACAACACTTAAATTAGGTTTAGT
1 TCATCACAAACAACACCTAAAACAGATTTAGAGTCATCACAAACAACACTCAAATTAGGTTTAGT
2125 A
66 A
* * * * * **
2126 TCATCACTAACAACATCTAAAACATATTTCGTGTCATTGCAAACAACACTCAAATTAGGTT
1 TCATCACAAACAACACCTAAAACAGATTTAGAGTCATCACAAACAACACTCAAATTAGGTT
2187 CAGAATTACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAGATTTAGAGTCATCACAAACAACACTCAAATTAGGTTTAGT
A
Found at i:5421 original size:22 final size:22
Alignment explanation
Indices: 5379--5421 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5369 TTTTCCGCAA
* *
5379 CAAGTCCTGGGCAAGAGTTGTC
1 CAAGTCCTGGACAAGACTTGTC
*
5401 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAAGACTTGT
5422 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAAGACTTGTC
Found at i:5477 original size:21 final size:21
Alignment explanation
Indices: 5451--5492 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5441 TTCAACAGAC
5451 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
*
5472 CAAGTCCTGGGTAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
5493 TCTGATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.26
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:5494 original size:71 final size:71
Alignment explanation
Indices: 5379--5563 Score: 280
Period size: 71 Copynumber: 2.6 Consensus size: 71
5369 TTTTCCGCAA
* * * *
5379 CAAGTCCTGGGCAAGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTTCATTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCATCTTTC
5444 AACAGAC
65 AACAGAC
* * * *
5451 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGTAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCATCTTTCA
5516 ACAGAC
66 ACAGAC
*
5522 CAGGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
5564 CCTGTTTTTA
Statistics
Matches: 102, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 82 0.80
72 20 0.20
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTTCCATCTTTCA
ACAGAC
Found at i:5551 original size:21 final size:21
Alignment explanation
Indices: 5525--5564 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5515 AACAGACCAG
*
5525 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
5546 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
5565 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:5636 original size:21 final size:21
Alignment explanation
Indices: 5611--5660 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5601 TTTTTCTTTG
*
5611 TTCAAATCATCTTCAAAT-GTC
1 TTCAAATCAACTTC-AATGGTC
* *
5632 TTCAATTGAACTTCAATGGTC
1 TTCAAATCAACTTCAATGGTC
5653 TTCAAATC
1 TTCAAATC
5661 TTCAAGATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (21 bp):
TTCAAATCAACTTCAATGGTC
Found at i:8679 original size:17 final size:17
Alignment explanation
Indices: 8649--8682 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8639 GTCAAATTTG
*
8649 AAGAAAAAATGAAAAAA
1 AAGAAAAAAGGAAAAAA
*
8666 AAGAAGAAAGGAAAAAA
1 AAGAAAAAAGGAAAAAA
8683 TGGAAAAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAGGAAAAAA
Found at i:9524 original size:23 final size:25
Alignment explanation
Indices: 9485--9538 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
9475 AAATGGTTGC
9485 TTTG-TTTTGTTTGTCTTGTT-TTA
1 TTTGCTTTTGTTTGTCTTGTTCTTA
*
9508 -TTGCTTTTGTTCT-TCTTTTTCTTA
1 TTTGCTTTTGTT-TGTCTTGTTCTTA
9532 TTTGCTT
1 TTTGCTT
9539 CACCCCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 13 0.50
24 4 0.15
25 6 0.23
ACGTcount: A:0.04, C:0.11, G:0.13, T:0.72
Consensus pattern (25 bp):
TTTGCTTTTGTTTGTCTTGTTCTTA
Found at i:11959 original size:14 final size:14
Alignment explanation
Indices: 11940--11967 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11930 AGCCAGATCG
11940 CAAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
11954 CAAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
11968 AACCAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:11960 original size:13 final size:13
Alignment explanation
Indices: 11942--11966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11932 CCAGATCGCA
11942 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
11955 AAAAAAAAAAAA
1 AAAAAAAAAAAA
11967 AAACCAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:11962 original size:16 final size:16
Alignment explanation
Indices: 11941--12009 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 16
11931 GCCAGATCGC
11941 AAAAAAAAAAAAACAA
1 AAAAAAAAAAAAACAA
*
11957 AAAAAAAAAAAAACCA
1 AAAAAAAAAAAAACAA
* * * *
11973 AGAACAACAACAACAA
1 AAAAAAAAAAAAACAA
** *
11989 AAAAACGACAAAACAA
1 AAAAAAAAAAAAACAA
12005 AAAAA
1 AAAAA
12010 GAGTGGAAAT
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAACAA
Found at i:13764 original size:67 final size:67
Alignment explanation
Indices: 13672--13798 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 67
13662 GAATGCCTTG
* * *
13672 GCTTTTCCACAAGCCAAACTTGTTTCCATATGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGC
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAGC
13737 AT
66 AT
* * *
13739 GCTTTTCCATAAGCCAAACTCGTTTCCGTACGAGTCAGTTGAAGCCTTGGTTCCACCCAA
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAA
13799 ACAATAGGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (67 bp):
GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAGC
AT
Found at i:13939 original size:105 final size:105
Alignment explanation
Indices: 13754--13942 Score: 245
Period size: 105 Copynumber: 1.8 Consensus size: 105
13744 TCCATAAGCC
* * *
13754 AAACTCGTTTCCGTACGAGTCAGTTGAAGCCTTGGTTCCACCCAAACAATAGGGGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAACAACAGGGGCTTTTCCATA
*
13819 AACCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AACCAACTTCATTTCCATATGAATTCAGTCTTCCAAGACT
* ** * * * *
13859 AAACTTGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATTCAAGCAGCATGTGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAACAACAGGGGCTTTTCCATA
* *
13924 AGCCAAACTT-GTTTCCATA
66 AACC-AACTTCATTTCCATA
13943 CGAGTCAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
105 66 0.94
106 4 0.06
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (105 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAACAACAGGGGCTTTTCCATA
AACCAACTTCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:15300 original size:15 final size:16
Alignment explanation
Indices: 15276--15315 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
15266 AGAGGTTGAA
*
15276 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
15291 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
15307 AGAAAACAA
1 AGAAAACAA
15316 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:19611 original size:15 final size:16
Alignment explanation
Indices: 19580--19619 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
19570 TTACTTTGCT
*
19580 TTGTTTTCTAGTTTAA
1 TTGTTTTCTACTTTAA
19596 TTGTTTTCT-CTTTAA
1 TTGTTTTCTACTTTAA
*
19611 TTGCTTTCT
1 TTGTTTTCT
19620 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTACTTTAA
Found at i:20070 original size:27 final size:27
Alignment explanation
Indices: 20028--20094 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
20018 GCATCTTTGA
20028 AAAAGAAAAAGAGTTTTCGT-TTTTGCGAT-
1 AAAA-AAAAA-AGTTTT-GTGTTTTGC-ATC
20057 AAAAAAAAAAGTTTTGTGTTTTGCATC
1 AAAAAAAAAAGTTTTGTGTTTTGCATC
20084 AAGAAAAAAAA
1 AA-AAAAAAAA
20095 AAATTGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
26 4 0.11
27 14 0.40
28 13 0.37
29 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.30
Consensus pattern (27 bp):
AAAAAAAAAAGTTTTGTGTTTTGCATC
Found at i:20281 original size:14 final size:14
Alignment explanation
Indices: 20258--20289 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
20248 CTACTAACAA
20258 TTTTTCTTTTGAGT
1 TTTTTCTTTTGAGT
*
20272 TTTTTTTTTTGAGT
1 TTTTTCTTTTGAGT
20286 TTTT
1 TTTT
20290 CTAGGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.03, G:0.12, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTTGAGT
Found at i:24339 original size:10 final size:10
Alignment explanation
Indices: 24324--24350 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
24314 GTAACACAAA
24324 TCACATACCT
1 TCACATACCT
24334 TCACATACCT
1 TCACATACCT
24344 TCACATA
1 TCACATA
24351 ATTCTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (10 bp):
TCACATACCT
Found at i:25088 original size:15 final size:16
Alignment explanation
Indices: 25058--25090 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
25048 TTACTTTGCT
25058 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
25074 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTTTAA
25089 TT
1 TT
25091 ACTTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:28929 original size:22 final size:24
Alignment explanation
Indices: 28892--28941 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
28882 AAAAAATTTA
28892 TTTATGACGCTGAAAAACT-TTTTT
1 TTTATGACGC-GAAAAACTCTTTTT
28916 TTTATGACGC-AAAAACTCTTTTT
1 TTTATGACGCGAAAAACTCTTTTT
28939 TTT
1 TTT
28942 TCAAAAACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.28
23 8 0.32
24 10 0.40
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (24 bp):
TTTATGACGCGAAAAACTCTTTTT
Found at i:28951 original size:26 final size:27
Alignment explanation
Indices: 28922--29028 Score: 74
Period size: 28 Copynumber: 3.7 Consensus size: 27
28912 TTTTTTTATG
*
28922 ACGCAAAAACTCTTTTTTTT-TCAAAA
1 ACGCAAAAACACTTTTTTTTATCAAAA
* *
28948 ACGCAACACAACAATTTTTTTTAAATTAAAA
1 ACGCAA-A-AACACTTTTTTTT--ATCAAAA
*
28979 ACGC-AAAACCCTTTTTTTTATGACGCAAAA
1 ACGCAAAAACACTTTTTTTTAT----CAAAA
* *
29009 ACACAAAAACAATTTTTTTT
1 ACGCAAAAACACTTTTTTTT
29029 TTTAGAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
26 8 0.13
27 1 0.02
28 22 0.35
29 1 0.02
30 8 0.13
31 22 0.35
ACGTcount: A:0.42, C:0.19, G:0.05, T:0.35
Consensus pattern (27 bp):
ACGCAAAAACACTTTTTTTTATCAAAA
Found at i:29386 original size:15 final size:16
Alignment explanation
Indices: 29362--29401 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
29352 AGAGGTTGAA
*
29362 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
29377 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
29393 AGAAAACAA
1 AGAAAACAA
29402 AACAAAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:31898 original size:12 final size:12
Alignment explanation
Indices: 31881--31906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31871 GCCGCAAGTT
31881 TTCATCTCTTTG
1 TTCATCTCTTTG
31893 TTCATCTCTTTG
1 TTCATCTCTTTG
31905 TT
1 TT
31907 GGCCTCCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (12 bp):
TTCATCTCTTTG
Found at i:35295 original size:21 final size:21
Alignment explanation
Indices: 35269--35310 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35259 TTTCGGGTCG
* *
35269 AAATTTTTTTTTTATTTTTTT
1 AAATTTTTTTTTGATATTTTT
35290 AAATTTTTTTTTGATATTTTT
1 AAATTTTTTTTTGATATTTTT
35311 CGATATAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
AAATTTTTTTTTGATATTTTT
Found at i:38395 original size:237 final size:237
Alignment explanation
Indices: 37975--38454 Score: 836
Period size: 237 Copynumber: 2.0 Consensus size: 237
37965 AAGGGGAGGG
*
37975 GATGATGCGGCAAGGACTTATCATGGACTTGAAGATGACAATGGAGATCATGGAAAGGATGAGCA
1 GATGATGCGCCAAGGACTTATCATGGACTTGAAGATGACAATGGAGATCATGGAAAGGATGAGCA
*
38040 AGGGCTGCAAGGAAGCATGGAGAAACATGAAGATCATGGAGATATCGTTGAGCATGTTCCAAGCA
66 AGGGCTGCAAGGAAGCATGGAGAAACATGAAGATCATGGAGATATCGTTGAGCATATTCCAAGCA
* * * * *
38105 CCAAGAAGATACCATTTGATCCATTAAAGATGCCTATTGGTCTGATGACAAGAGCAAGAGCTACG
131 CCAAGAAGATACCATTTGATCCATTAAAGATGCATATCGGTCCGATAACAAGAGCAAGAGCTAAG
38170 AGCTTCAAGGATGCACTCATGGGCCTTGTTCGAAGTCATCTA
196 AGCTTCAAGGATGCACTCATGGGCCTTGTTCGAAGTCATCTA
*
38212 GATGATGCGCCAATGG-CTTATCATGGACTTGAAGATGACAATGTAGATCATGGAAAGGATGAGC
1 GATGATGCGCCAA-GGACTTATCATGGACTTGAAGATGACAATGGAGATCATGGAAAGGATGAGC
*
38276 AAGGGCTGCAAGGAAGCATGGAGAAGCATGAAGATCATGGAGATATCGTTGAGCATATTCCAAGC
65 AAGGGCTGCAAGGAAGCATGGAGAAACATGAAGATCATGGAGATATCGTTGAGCATATTCCAAGC
**
38341 ACCAAGAAGATGTCATTTGATCCATTAAAGATGCATATCGGTCCGATAACAAGAGCAAGAGCTAA
130 ACCAAGAAGATACCATTTGATCCATTAAAGATGCATATCGGTCCGATAACAAGAGCAAGAGCTAA
*
38406 GAGGTTCAAGGATGCACTCATGGGCCTTGTTCGAAGTCATCTA
195 GAGCTTCAAGGATGCACTCATGGGCCTTGTTCGAAGTCATCTA
38449 GATGAT
1 GATGAT
38455 ATGAAAGTCA
Statistics
Matches: 230, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
237 228 0.99
238 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (237 bp):
GATGATGCGCCAAGGACTTATCATGGACTTGAAGATGACAATGGAGATCATGGAAAGGATGAGCA
AGGGCTGCAAGGAAGCATGGAGAAACATGAAGATCATGGAGATATCGTTGAGCATATTCCAAGCA
CCAAGAAGATACCATTTGATCCATTAAAGATGCATATCGGTCCGATAACAAGAGCAAGAGCTAAG
AGCTTCAAGGATGCACTCATGGGCCTTGTTCGAAGTCATCTA
Found at i:39412 original size:478 final size:484
Alignment explanation
Indices: 38504--39460 Score: 1357
Period size: 478 Copynumber: 2.0 Consensus size: 484
38494 GATTTGAGCA
*
38504 AGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGATATTACTTAGGGCTTGAAT
1 AGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGATATGACTT---GCTTGAAT
38569 GTATAATTTCGGCTATTGTGGGCTTTATTCTATCTTAAATTAGCTTATTGTTATGTTTAGATGAC
63 GTATAATTTCGGCTATTGTGGGCTTTATTCTATCTTAAATTAGCTTATTGTTATGTTTAGATGAC
* * *
38634 ATTAGGATTGGGCATTGTTTGACTAAGTCCAATCCTTGTTTAATTATGCCTTGTTATTTATTTTT
128 ATTAGGATTGGGCATTCTTTGACTAAGCCCAATCCTTGTATAATTATGCCTTGTTATTTATTTTT
* * *
38699 CCTAGTTGGACTTGGATTAGTTTTCCTTGTCTTTATTTTTGGGCTTGTAAGGCTTGATAGCCGCC
193 CCTAGTTGGACTTCGATTAGTTTTCCTTGTCCTTATTTTT--G-ATGTAAGGC-TGATAGCCGCC
* * * *
38764 CATACCTCTTTAGAATTAGGGTTAGGACGTCCCTTACTACTATACAAGGGATCCATACCCCTCTT
254 CATACCGCTTTAGAATTAGGATTAGGACGACCCCTACTACTATACAAGGGATCCATACCCCTCTT
*
38829 GTAAACACAAGTTAAGTTTTTCAATCAAAGAGATTTCTTTTGAGAATTTAGCTTCATTGTTCTAG
319 GTAAACACAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGAATTTAGCTTCATTGTTCTAG
*
38894 TTTGAACATACTTAGGATTTCTTCAATTTTGTAAAGTCCTAGCAAACAATGAGATAGTGATTAT-
384 TTTGAACATACTTAGGATTTCTTCAATTTTGTAAAGTCCTAGCAAACAATGAGATAATGATTATC
*
38958 TAAATTGTGTTTCTTGTGAT-TTAGATGATCAATTAG
449 T-AATTATGTTTCTTGTGATCTTAGATGATCAATTAG
38994 AGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGATATGACTT-CTTGAATGTA
1 AGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGATATGACTTGCTTGAATGTA
* *
39058 TAATTTCGGCTATTGTGGGCTTTATTCTATCTTAGATTAGCTTTTTTGTTATGTTTAGATGACAT
66 TAATTTCGGCTATTGTGGGCTTTATTCTATCTTAAATTAGC-TTATTGTTATGTTTAGATGACAT
* *
39123 TAGGATTGGG-ACTTCTTTGACTAAGCCCAATCCTTGTATAATTATGTCTTGTTTTTTATTTTTC
130 TAGGATTGGGCA-TTCTTTGACTAAGCCCAATCCTTGTATAATTATGCCTTGTTATTTATTTTTC
*
39187 CTAGTTGGACTTCGATTAGGCTTTTCCTTGTCCTTA-TTTT-AT-T-ATG-TG-T-GCCGCCCAT
194 CTAGTTGGACTTCGATTA-G-TTTTCCTTGTCCTTATTTTTGATGTAAGGCTGATAGCCGCCCAT
** ** *** * * ** * *
39245 AGGGCTTTA-TTTTCTTATCTAGGTCGACCCCTA-TGCCTATTTAAGGGACTCGA-CCCCCTCTT
257 ACCGCTTTAGAATTAGGAT-TAGGACGACCCCTACT-ACTATACAAGGGA-TCCATACCCCTCTT
*
39307 GTAAACTCAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGAATTTAGCTTCATTGTTCTAG
319 GTAAACACAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGAATTTAGCTTCATTGTTCTAG
* *
39372 TTTGAACATACTTAGGATTTCTTCAATTTTGTAGAGTCCTAGCAAACAATTAGATAATGATTATC
384 TTTGAACATACTTAGGATTTCTTCAATTTTGTAAAGTCCTAGCAAACAATGAGATAATGATTATC
*
39437 TAGTTATGTTTCTTGTGATCTTAG
449 TAATTATGTTTCTTGTGATCTTAG
39461 GTTGTCAATT
Statistics
Matches: 422, Mismatches: 36, Indels: 29
0.87 0.07 0.06
Matches are distributed among these distances:
477 4 0.01
478 184 0.44
479 9 0.02
480 2 0.00
482 2 0.00
483 1 0.00
484 1 0.00
486 51 0.12
487 96 0.23
488 5 0.01
489 14 0.03
490 53 0.13
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (484 bp):
AGCATTCATCCATTGATTCCAAGATCATCACCTTACTTGCAATCGATATGACTTGCTTGAATGTA
TAATTTCGGCTATTGTGGGCTTTATTCTATCTTAAATTAGCTTATTGTTATGTTTAGATGACATT
AGGATTGGGCATTCTTTGACTAAGCCCAATCCTTGTATAATTATGCCTTGTTATTTATTTTTCCT
AGTTGGACTTCGATTAGTTTTCCTTGTCCTTATTTTTGATGTAAGGCTGATAGCCGCCCATACCG
CTTTAGAATTAGGATTAGGACGACCCCTACTACTATACAAGGGATCCATACCCCTCTTGTAAACA
CAAGTTAAGTTTTTCAATCAAAGAGAGTTCTTTTGAGAATTTAGCTTCATTGTTCTAGTTTGAAC
ATACTTAGGATTTCTTCAATTTTGTAAAGTCCTAGCAAACAATGAGATAATGATTATCTAATTAT
GTTTCTTGTGATCTTAGATGATCAATTAG
Found at i:40922 original size:17 final size:16
Alignment explanation
Indices: 40884--40934 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
40874 AAATTAACTT
40884 TTATTTTTTTCTTTT-
1 TTATTTTTTTCTTTTC
* *
40899 TTCTTTTTTCCCTTTTC
1 TTATTTTTT-TCTTTTC
40916 TTATTTTTTTTCTTTTC
1 TTA-TTTTTTTCTTTTC
40933 TT
1 TT
40935 CTCTCTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.28
16 5 0.17
17 10 0.34
18 6 0.21
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (16 bp):
TTATTTTTTTCTTTTC
Found at i:41632 original size:23 final size:23
Alignment explanation
Indices: 41602--41645 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41592 TTTTGTGTTC
*
41602 TTGAGTTCTTTGGAAAATGATCT
1 TTGAGTTCTTAGGAAAATGATCT
41625 TTGAGTTCTTAGGAAAATGAT
1 TTGAGTTCTTAGGAAAATGAT
41646 AGTTTTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (23 bp):
TTGAGTTCTTAGGAAAATGATCT
Found at i:47470 original size:29 final size:30
Alignment explanation
Indices: 47437--47506 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
47427 CATTAGGATG
* *
47437 TTTTGTCCCCTGGACT-TTAATTTTGCACA
1 TTTTGCCCCCTGAACTCTTAATTTTGCACA
* * *
47466 TTTTGCCCCCTTAACTCTTAATTTTGGATA
1 TTTTGCCCCCTGAACTCTTAATTTTGCACA
47496 TTTTGCCCCCT
1 TTTTGCCCCCT
47507 CTCAAAACGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 13 0.37
30 22 0.63
ACGTcount: A:0.16, C:0.27, G:0.11, T:0.46
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTCTTAATTTTGCACA
Found at i:47666 original size:30 final size:29
Alignment explanation
Indices: 47630--47769 Score: 136
Period size: 31 Copynumber: 4.7 Consensus size: 29
47620 ATCCTTTGAG
*
47630 AGGGGGCAAAACATCCAAAATTGAGAGTTA
1 AGGGGGCAAAACGTCCAAAATTGA-AGTTA
* *
47660 AGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAAGTTA
* ** *
47689 AGGGGGCAAAACGTCCAAACGCTACAAGTTC
1 AGGGGGCAAAACGTCCAAA--ATTGAAGTTA
* ** *
47720 AGGGGGCAAAACGTCCAAACGCTACAAGTTC
1 AGGGGGCAAAACGTCCAAA--ATTGAAGTTA
47751 AGGGGGCAAAACGTCCAAA
1 AGGGGGCAAAACGTCCAAA
47770 CGCTACAAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
29 22 0.22
30 22 0.22
31 57 0.56
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTGAAGTTA
Found at i:47721 original size:31 final size:31
Alignment explanation
Indices: 47683--47792 Score: 220
Period size: 31 Copynumber: 3.5 Consensus size: 31
47673 TCCAAAATTG
47683 AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
1 AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
47714 AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
1 AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
47745 AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
1 AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
47776 AAGTTCAGGGGGCAAAA
1 AAGTTCAGGGGGCAAAA
47793 AGGGTATTAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.36, C:0.24, G:0.27, T:0.13
Consensus pattern (31 bp):
AAGTTCAGGGGGCAAAACGTCCAAACGCTAC
Found at i:54718 original size:24 final size:26
Alignment explanation
Indices: 54673--54721 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
54663 ATTGCCATAG
54673 TTTAGATTTAATTACTTTTCTTTATT
1 TTTAGATTTAATTACTTTTCTTTATT
*
54699 TTTAG-TTTAATT-GTTTTCTTTAT
1 TTTAGATTTAATTACTTTTCTTTAT
54722 AATTGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTAGATTTAATTACTTTTCTTTATT
Found at i:55686 original size:75 final size:76
Alignment explanation
Indices: 55607--55821 Score: 204
Period size: 75 Copynumber: 2.9 Consensus size: 76
55597 GAAACAACAT
* * **
55607 CCTGATTAGGAGAATCAACTTCAAGATGTTGCCTATCATCATTATG-ATGCTCAAAATTTGAATT
1 CCTGATTAGGTGAATCAACTTCAAGATATTGCCTATCATCA-TATGAAAACTCAAAATTTGAATT
*
55671 CAAATC-AGAAA
65 CAAAACAAGAAA
* * * ** * * **
55682 CCTGATAAAGTGAATCAGCTTCAAGATATTGCAAATCATCATCTGAAAACTTAGTATTTGAATTC
1 CCTGATTAGGTGAATCAACTTCAAGATATTGCCTATCATCATATGAAAACTCAAAATTTGAATTC
55747 AAAACAAGAAA
66 AAAACAAGAAA
* * * * **
55758 -CTGATTAGGTGAATCATCTTCAAGATTTTGCCTAACACCATCA-GAAAACTCATTATTTGAATT
1 CCTGATTAGGTGAATCAACTTCAAGATATTGCCTATCATCAT-ATGAAAACTCAAAATTTGAATT
55821 C
65 C
55822 GAATTAGCAA
Statistics
Matches: 112, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
74 3 0.03
75 104 0.93
76 5 0.04
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (76 bp):
CCTGATTAGGTGAATCAACTTCAAGATATTGCCTATCATCATATGAAAACTCAAAATTTGAATTC
AAAACAAGAAA
Found at i:63176 original size:6 final size:6
Alignment explanation
Indices: 63167--63193 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
63157 ACCAAAAGCA
63167 AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA
63194 TAAATAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:70103 original size:21 final size:21
Alignment explanation
Indices: 70078--70119 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
70068 TTTGGAGCTC
70078 ATTGAATTCAAAATTAAGGTT
1 ATTGAATTCAAAATTAAGGTT
* *
70099 ATTGAGTTCAAAATTAGGGTT
1 ATTGAATTCAAAATTAAGGTT
70120 CTTAGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (21 bp):
ATTGAATTCAAAATTAAGGTT
Done.