Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018128.1 Corchorus olitorius cultivar O-4 contig18161, 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: 71673
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2114 original size:29 final size:29
Alignment explanation
Indices: 2050--2150 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 29
2040 TCTGTTTTGT
** *
2050 CCTTATTTGACCCAAATTGAAAATGTTAGGC
1 CCTTATTTGA-CCTTATTG-AAAGGTTAGGC
*
2081 ACTTATTTGACCTTATTGAAAGGTTAGGC
1 CCTTATTTGACCTTATTGAAAGGTTAGGC
** * * *
2110 CCTTAAATGACCTTTTCCTTAAAGGTCAGGC
1 CCTTATTTGACCTTAT--TGAAAGGTTAGGC
*
2141 CCCTATTTGA
1 CCTTATTTGA
2151 ACTTTTAACC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 22 0.40
30 6 0.11
31 27 0.49
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (29 bp):
CCTTATTTGACCTTATTGAAAGGTTAGGC
Found at i:6307 original size:46 final size:46
Alignment explanation
Indices: 6254--6347 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
6244 CCAAGAAGAT
* *
6254 AAGTGCAACCTGATAGTACAATGTAAGTATGTGAGAATTTAGAACA
1 AAGTGCAACCTGATAGTACAACGTAAGTATGAGAGAATTTAGAACA
6300 AAGTGCAACCTGATAGTACAACGTAAGTATGAGAGAATTTAGAACA
1 AAGTGCAACCTGATAGTACAACGTAAGTATGAGAGAATTTAGAACA
6346 AA
1 AA
6348 ATAAAACCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (46 bp):
AAGTGCAACCTGATAGTACAACGTAAGTATGAGAGAATTTAGAACA
Found at i:9175 original size:14 final size:14
Alignment explanation
Indices: 9152--9184 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
9142 TGTTCCACCC
*
9152 TTTATGTATTTATA
1 TTTATATATTTATA
9166 TTTATATATTTATA
1 TTTATATATTTATA
9180 TTTAT
1 TTTAT
9185 TTTATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTATATATTTATA
Found at i:13107 original size:128 final size:123
Alignment explanation
Indices: 12840--13156 Score: 327
Period size: 124 Copynumber: 2.5 Consensus size: 123
12830 GACATATATG
* * * * * *
12840 TGTTGCCTCGTTAAAAACCTTAAGTCGGAAAAATCTAGTGGGACAAAATCCGGACATAAGGGAAA
1 TGTTGCCTCATTAAAAACCTTAAGTCGG-AAAACCCAGTGGGACAAAAACCGAACATAAAGGAAA
* * * * * * *
12905 AAAAGTACAACATTGTCCCTCTAATTTGTCTTCATGACAATATTAATTTGATGTGTTAT
65 AAAACTACAACATTGTCCATCTAATATGTCTTCAGGACAATATCAATTAGATGTGTGAT
** * *
12964 TGCCGCCTCATTAAAAACCTTAAGTCGGTAAAACCCAGTGGGATAAAAACCGAATATAAAGGAAA
1 TGTTGCCTCATTAAAAACCTTAAGTCGG-AAAACCCAGTGGGACAAAAACCGAACATAAAGGAAA
* *
13029 AATACTACAGAGCAATTAAGTCCATGTAA-ATGTCTTCAGGACAAT-TCAATCTAGATGTGCTGA
65 AAAACTACA-A-C-ATT--GTCCATCTAATATGTCTTCAGGACAATATCAAT-TAGATGTG-TGA
13092 -
123 T
** *
13092 TGTTGCCTCATTAAAAACCTTAAGTCGGAAAACCCAGTGGGAC-AAAACCGTTCATAAGGGAAAA
1 TGTTGCCTCATTAAAAACCTTAAGTCGGAAAACCCAGTGGGACAAAAACCGAACATAAAGGAAAA
13156 A
66 A
13157 GAGTGCAACA
Statistics
Matches: 159, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
124 61 0.38
125 1 0.01
126 19 0.12
127 21 0.13
128 47 0.30
129 10 0.06
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (123 bp):
TGTTGCCTCATTAAAAACCTTAAGTCGGAAAACCCAGTGGGACAAAAACCGAACATAAAGGAAAA
AAACTACAACATTGTCCATCTAATATGTCTTCAGGACAATATCAATTAGATGTGTGAT
Found at i:13239 original size:25 final size:25
Alignment explanation
Indices: 13210--13259 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13200 AAAGAAACAA
* *
13210 CCACTTCTGGGGTATCCAAACATTT
1 CCACTTCTGGAGAATCCAAACATTT
*
13235 CCACTTCTGGAGAATTCAAACATTT
1 CCACTTCTGGAGAATCCAAACATTT
13260 TACTAGCTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (25 bp):
CCACTTCTGGAGAATCCAAACATTT
Found at i:26497 original size:25 final size:24
Alignment explanation
Indices: 26455--26502 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
26445 TGTGCCACTA
*
26455 CAGGGGCAATATGCTCATGACTCTT
1 CAGGGGCAATATGATCATG-CTCTT
*
26480 CAGGGGCAATATTATCATGCTCT
1 CAGGGGCAATATGATCATGCTCT
26503 CTATACTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (24 bp):
CAGGGGCAATATGATCATGCTCTT
Found at i:29735 original size:21 final size:21
Alignment explanation
Indices: 29709--29749 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29699 TTTAAACCCT
29709 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
29730 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
29750 GGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:35747 original size:51 final size:51
Alignment explanation
Indices: 35682--36066 Score: 623
Period size: 50 Copynumber: 7.6 Consensus size: 51
35672 CGATCAACTT
*
35682 CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
* *
35733 CTTTGAACTGTCTTCCAATTCAAGCTTAAAACGGACCATCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
*
35784 TTCTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
1 --CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
* *
35837 TTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
35887 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
* *
35938 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCTGCTTATC
1 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
* *
35988 CTTTGAACTGTCTTCTAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
* *
36038 CTTTGAATTGTCTTCCAATTCAATCTTAA
1 CTTTGAACTGTCTTCCAATTCAAGCTTAA
36067 GAAAATCATC
Statistics
Matches: 313, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
50 143 0.46
51 122 0.39
53 48 0.15
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (51 bp):
CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATC
Found at i:35850 original size:23 final size:23
Alignment explanation
Indices: 35823--35902 Score: 61
Period size: 23 Copynumber: 3.3 Consensus size: 23
35813 AAAAAGGACC
35823 GTCTTCCGCTTATCTTTTGAACT
1 GTCTTCCGCTTATCTTTTGAACT
** ** * *
35846 GTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCGCTT--ATCTT--TTGAACT
*
35873 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCTTTTGAACT
35896 GTCTTCC
1 GTCTTCC
35903 AATTCAAGCT
Statistics
Matches: 40, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
23 19 0.47
25 9 0.22
27 12 0.30
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (23 bp):
GTCTTCCGCTTATCTTTTGAACT
Found at i:35943 original size:101 final size:101
Alignment explanation
Indices: 35682--36066 Score: 655
Period size: 101 Copynumber: 3.8 Consensus size: 101
35672 CGATCAACTT
35682 CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
1 CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
* *
35747 CCAATTCAAGCTTAAAACGGACCATCTTCCGCTTATC
66 CCAATTCAATCTTAAAA-GGACCGTCTTCCGCTTATC
*
35784 TTCTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCTTTTGAACTGTC
1 --CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTC
35849 TTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
64 TTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
35887 CTTTGAACTGTCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
1 CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
*
35952 CCAATTCAATCTTAAAAGGACCGTCTTCTGCTTATC
66 CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * * *
35988 CTTTGAACTGTCTTCTAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATCCTTTGAATTGTCTT
1 CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
36052 CCAATTCAATCTTAA
66 CCAATTCAATCTTAA
36067 GAAAATCATC
Statistics
Matches: 272, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
100 51 0.19
101 123 0.45
103 18 0.07
104 80 0.29
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.36
Consensus pattern (101 bp):
CTTTGAACTATCTTCCAATTCAAGCTTAAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTT
CCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:36118 original size:14 final size:15
Alignment explanation
Indices: 36088--36124 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
36078 TTTGATGCTC
36088 TTTGA-AAAGATTCA
1 TTTGAGAAAGATTCA
*
36102 TTTGAGAAAG-TTTA
1 TTTGAGAAAGATTCA
36116 TTTGAGAAA
1 TTTGAGAAA
36125 AGTCGTCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (15 bp):
TTTGAGAAAGATTCA
Found at i:36482 original size:64 final size:64
Alignment explanation
Indices: 36294--36696 Score: 531
Period size: 64 Copynumber: 6.3 Consensus size: 64
36284 AGTGCATCTC
* * * * * *
36294 TTAACAAGATCGTCTTCCGACCAACTTCTGAAACCTTTTCGAGAAACTATATGCTGGTGTACTTT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTT-GAGAAACCATCTTCTGGTGTACTTT
* * *
36359 TTAACAAGATCGCCTTCCGATCAACTT-TGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTT
*
36422 TTAACAAGATCGTCTTCTGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTT-T
** * * * * *
36487 TTAATGAGATTGTCTTCCAATCAAATT-TGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTT
* *
36550 TTAACAAGATCGTCTTGCGATCAAATTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCT
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTT-T
** * * *
36615 TTAATGAGATTGTCTTCCAATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTC
1 TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTT
**
36679 TTAATGAGATCGTCTTCC
1 TTAACAAGATCGTCTTCC
36697 AATCCATACT
Statistics
Matches: 299, Mismatches: 35, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
63 68 0.23
64 128 0.43
65 103 0.34
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (64 bp):
TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTT
Found at i:36510 original size:128 final size:127
Alignment explanation
Indices: 36294--36695 Score: 599
Period size: 128 Copynumber: 3.1 Consensus size: 127
36284 AGTGCATCTC
* * * * * *
36294 TTAACAAGATCGTCTTCCGACCAACTTCTGAAACCTTTTCGAGAAACTATATGCTGGTGTACTT-
1 TTAACAAGATCGTCTT-CGATCAACTTCTGAAAACTGTT-GAGAAACCATCTTCTGGTGTACTTC
** * * *
36358 TTTAACAAGATCGCCTTCCGATCAACTTTGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
64 TTTAATGAGATTGTCTTCCAATCAACTTTGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
36422 TTAACAAGATCGTCTTCTGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCT
1 TTAACAAGATCGTCTTC-GATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCT
*
36487 TTAATGAGATTGTCTTCCAATCAAATTTGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
65 TTAATGAGATTGTCTTCCAATCAACTTTGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
*
36550 TTAACAAGATCGTCTTGCGATCAAATTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCT
1 TTAACAAGATCGTCTT-CGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCT
* *
36615 TTAATGAGATTGTCTTCCAATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTC
65 TTAATGAGATTGTCTTCCAATCAACTT-TGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
**
36679 TTAATGAGATCGTCTTC
1 TTAACAAGATCGTCTTC
36696 CAATCCATAC
Statistics
Matches: 252, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
127 22 0.09
128 181 0.72
129 49 0.19
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (127 bp):
TTAACAAGATCGTCTTCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCTT
TAATGAGATTGTCTTCCAATCAACTTTGAAAACTATTGAGAAACCATCTTCTGGTGTACTTG
Found at i:36752 original size:67 final size:67
Alignment explanation
Indices: 36464--36802 Score: 251
Period size: 64 Copynumber: 5.2 Consensus size: 67
36454 AACTGTTGAG
* * * *
36464 AAACCATCTTCTGGTGTACTTCTTTAATGAGATTGTCTTCCAATCAA-ATTTGAAAA--CTATT-
1 AAACCATCTTCCGGTGTACTTC-TTAATGAGATCGCCTTCCAATCAACACTTGAAAATTCT-TTC
*
36525 GAG-
64 TAGC
* * ** * * * *
36528 AAACCATCTTCTGGTGTACTTGTTAACAAGATCGTCTTGCGATCAA-ATTCTGAAAA--CTGTT-
1 AAACCATCTTCCGGTGTACTTCTTAATGAGATCGCCTTCCAATCAACACT-TGAAAATTCT-TTC
*
36589 GAG-
64 TAGC
* * * *
36592 AAACCATCTTCTGGTGTACTTCTTTAATGAGATTGTCTTCCAATCAAC-TTCTGAAAA--CTGTT
1 AAACCATCTTCCGGTGTACTTC-TTAATGAGATCGCCTTCCAATCAACACT-TGAAAATTCT-TT
*
36654 -GAG-
63 CTAGC
* * * * *
36657 AAACCATCTTCTGGTGTACTTCTTAATGAGATCGTCTTCCAATCCATACTTGAAAGTTCTTTCTA
1 AAACCATCTTCCGGTGTACTTCTTAATGAGATCGCCTTCCAATCAACACTTGAAAATTCTTTCTA
36722 GC
66 GC
* * *
36724 AAACCGTCTTCCGGTGTA-TTCCTTAATGAGATGGCCTTCCAATCAACATTTGAAAATTCTTTCT
1 AAACCATCTTCCGGTGTACTT-CTTAATGAGATCGCCTTCCAATCAACACTTGAAAATTCTTTCT
36788 AGC
65 AGC
36791 AAACCATCTTCC
1 AAACCATCTTCC
36803 AATGTGCTTC
Statistics
Matches: 238, Mismatches: 28, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
63 22 0.09
64 82 0.34
65 61 0.26
66 6 0.03
67 67 0.28
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (67 bp):
AAACCATCTTCCGGTGTACTTCTTAATGAGATCGCCTTCCAATCAACACTTGAAAATTCTTTCTA
GC
Found at i:48111 original size:12 final size:13
Alignment explanation
Indices: 48093--48122 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
48083 GTTTTCTTTA
48093 ATTTTCTTGATTG
1 ATTTTCTTGATTG
48106 -TTTTCTTGATTG
1 ATTTTCTTGATTG
48118 ATTTT
1 ATTTT
48123 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:49687 original size:19 final size:18
Alignment explanation
Indices: 49663--49698 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
49653 TGAAGACTTA
49663 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
49682 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
49699 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:51352 original size:21 final size:22
Alignment explanation
Indices: 51328--51370 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
51318 TTCATCTGAT
* *
51328 TTCATTGATTTTTTC-GATTTC
1 TTCATTCATTTTCTCAGATTTC
51349 TTCATTCATTTTCTCAGATTTC
1 TTCATTCATTTTCTCAGATTTC
51371 CTTGTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.16, C:0.19, G:0.07, T:0.58
Consensus pattern (22 bp):
TTCATTCATTTTCTCAGATTTC
Found at i:57011 original size:334 final size:334
Alignment explanation
Indices: 56402--57071 Score: 1340
Period size: 334 Copynumber: 2.0 Consensus size: 334
56392 TTCTGGATTC
56402 GTGCAGGGACTTCGATGGCAATTTTGGGCTTGAAGATGGCAGAACTGGGCCTTGGACTTCAAAGG
1 GTGCAGGGACTTCGATGGCAATTTTGGGCTTGAAGATGGCAGAACTGGGCCTTGGACTTCAAAGG
56467 AAAGTTGTAGATCTCTGAGTTAGCTTTCCAACGGCTACTCACGGGTCTAAAACGGACATCTGAGC
66 AAAGTTGTAGATCTCTGAGTTAGCTTTCCAACGGCTACTCACGGGTCTAAAACGGACATCTGAGC
56532 AGAAAGTTATGATTTGTCTACCGAGACTGCGCTGAATCCTAATCCTGTTAGGACTAGAAACGGGA
131 AGAAAGTTATGATTTGTCTACCGAGACTGCGCTGAATCCTAATCCTGTTAGGACTAGAAACGGGA
56597 ATATGCGGAAATTGGATATTTCCTTGGATATAGGAGGCACAAATTGAGTTTTTAATTCCAATTAT
196 ATATGCGGAAATTGGATATTTCCTTGGATATAGGAGGCACAAATTGAGTTTTTAATTCCAATTAT
56662 GGACTTATATGGGCTGAGTATAATCCCATATAAAATATCCAAAATTCCAAAGCTTCTAGGCTTTT
261 GGACTTATATGGGCTGAGTATAATCCCATATAAAATATCCAAAATTCCAAAGCTTCTAGGCTTTT
56727 TCATGGGTT
326 TCATGGGTT
56736 GTGCAGGGACTTCGATGGCAATTTTGGGCTTGAAGATGGCAGAACTGGGCCTTGGACTTCAAAGG
1 GTGCAGGGACTTCGATGGCAATTTTGGGCTTGAAGATGGCAGAACTGGGCCTTGGACTTCAAAGG
56801 AAAGTTGTAGATCTCTGAGTTAGCTTTCCAACGGCTACTCACGGGTCTAAAACGGACATCTGAGC
66 AAAGTTGTAGATCTCTGAGTTAGCTTTCCAACGGCTACTCACGGGTCTAAAACGGACATCTGAGC
56866 AGAAAGTTATGATTTGTCTACCGAGACTGCGCTGAATCCTAATCCTGTTAGGACTAGAAACGGGA
131 AGAAAGTTATGATTTGTCTACCGAGACTGCGCTGAATCCTAATCCTGTTAGGACTAGAAACGGGA
56931 ATATGCGGAAATTGGATATTTCCTTGGATATAGGAGGCACAAATTGAGTTTTTAATTCCAATTAT
196 ATATGCGGAAATTGGATATTTCCTTGGATATAGGAGGCACAAATTGAGTTTTTAATTCCAATTAT
56996 GGACTTATATGGGCTGAGTATAATCCCATATAAAATATCCAAAATTCCAAAGCTTCTAGGCTTTT
261 GGACTTATATGGGCTGAGTATAATCCCATATAAAATATCCAAAATTCCAAAGCTTCTAGGCTTTT
57061 TCATGGGTT
326 TCATGGGTT
57070 GT
1 GT
57072 CTTCAATCCT
Statistics
Matches: 336, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 336 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (334 bp):
GTGCAGGGACTTCGATGGCAATTTTGGGCTTGAAGATGGCAGAACTGGGCCTTGGACTTCAAAGG
AAAGTTGTAGATCTCTGAGTTAGCTTTCCAACGGCTACTCACGGGTCTAAAACGGACATCTGAGC
AGAAAGTTATGATTTGTCTACCGAGACTGCGCTGAATCCTAATCCTGTTAGGACTAGAAACGGGA
ATATGCGGAAATTGGATATTTCCTTGGATATAGGAGGCACAAATTGAGTTTTTAATTCCAATTAT
GGACTTATATGGGCTGAGTATAATCCCATATAAAATATCCAAAATTCCAAAGCTTCTAGGCTTTT
TCATGGGTT
Found at i:66575 original size:19 final size:18
Alignment explanation
Indices: 66542--66577 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
66532 TTGAGATAAT
66542 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
66560 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
66578 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Done.