Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019794.1 Corchorus olitorius cultivar O-4 contig19827, 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: 43871
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:119 original size:15 final size:15
Alignment explanation
Indices: 99--130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
89 AGAGGAGGAG
99 AAGGAAAAAAAGAAA
1 AAGGAAAAAAAGAAA
*
114 AAGGAAAAAAGGAAA
1 AAGGAAAAAAAGAAA
129 AA
1 AA
131 AATCAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGGAAAAAAAGAAA
Found at i:240 original size:31 final size:31
Alignment explanation
Indices: 174--255 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 31
164 ACTAAATACT
*
174 AAAAAAATCCCTAATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
205 -AAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
*
235 AAAAAAATCCCTTATATTTTT
1 AAAAAAATCCCTTATGTTTTT
256 TTTGGACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 29 0.60
31 19 0.40
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
Found at i:452 original size:29 final size:30
Alignment explanation
Indices: 420--477 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
410 AACGTAAGGG
* *
420 ATTAATTTGTCTCGAAA-AAAACATAAGAA
1 ATTAATTTGTCCCAAAACAAAACATAAGAA
*
449 ATTATTTTGTCCCAAAAGCAAAACATAAG
1 ATTAATTTGTCCCAAAA-CAAAACATAAG
478 GGATTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 14 0.58
31 10 0.42
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (30 bp):
ATTAATTTGTCCCAAAACAAAACATAAGAA
Found at i:6790 original size:24 final size:25
Alignment explanation
Indices: 6761--6811 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
6751 ATAGAGTAAC
* *
6761 AATAAAATAAATAAGCAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
6785 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
6810 AA
1 AA
6812 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:6851 original size:13 final size:13
Alignment explanation
Indices: 6830--6860 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6820 ATCCTAAGCA
*
6830 TTGACTATTCAGG
1 TTGATTATTCAGG
6843 TTGATTATTCAGG
1 TTGATTATTCAGG
6856 TTGAT
1 TTGAT
6861 CTAATCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (13 bp):
TTGATTATTCAGG
Found at i:7722 original size:22 final size:22
Alignment explanation
Indices: 7697--7738 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7687 GTGTTCCTGA
*
7697 GGGTACTCGGGGCCGGGTAGGG
1 GGGTACCCGGGGCCGGGTAGGG
7719 GGGTACCCGGGGCCGGGTAG
1 GGGTACCCGGGGCCGGGTAG
7739 CCTCAGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.57, T:0.12
Consensus pattern (22 bp):
GGGTACCCGGGGCCGGGTAGGG
Found at i:9013 original size:37 final size:38
Alignment explanation
Indices: 8963--9041 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
8953 ATATAATTAT
* *
8963 TCATAAAATTATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAATTATGTCTATATGAAAAGACATGATGTTGA
*
9000 TCATAAAGTTATGTCTATATGAAAAGACATGTATGTTGA
1 TCATAAAATTATGTCTATATGAAAAGACATG-ATGTTGA
9039 TCA
1 TCA
9042 AGTATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 28 0.76
39 9 0.24
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (38 bp):
TCATAAAATTATGTCTATATGAAAAGACATGATGTTGA
Found at i:10392 original size:20 final size:20
Alignment explanation
Indices: 10367--10407 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
10357 AGAGTGTAGT
*
10367 ACAATTTATTGCTGAAAGTC
1 ACAATTTATTGATGAAAGTC
10387 ACAATTTATTGATGAAAGTC
1 ACAATTTATTGATGAAAGTC
10407 A
1 A
10408 TTGGAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (20 bp):
ACAATTTATTGATGAAAGTC
Found at i:11567 original size:37 final size:37
Alignment explanation
Indices: 11517--11587 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
11507 ATATAATTAT
* *
11517 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
11554 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
11588 GTTGATCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:18523 original size:50 final size:50
Alignment explanation
Indices: 18464--18566 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
18454 AAGCTTAGTC
18464 GTGTTTGTCTAGTTAATGTGGATTGCTTGGTATTGTTGGAGTGATATTCA
1 GTGTTTGTCTAGTTAATGTGGATTGCTTGGTATTGTTGGAGTGATATTCA
18514 GTGTTTGTCTAGTTAATGTGGATTGCTTGGTATTGTTGGAGTGATATTCA
1 GTGTTTGTCTAGTTAATGTGGATTGCTTGGTATTGTTGGAGTGATATTCA
18564 GTG
1 GTG
18567 AACGTAAACT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (50 bp):
GTGTTTGTCTAGTTAATGTGGATTGCTTGGTATTGTTGGAGTGATATTCA
Found at i:19301 original size:31 final size:32
Alignment explanation
Indices: 19250--19310 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
19240 CGTGTTCCAA
* *
19250 TCCGTGCCTGAACTTCAGGCA-TGGCATAAGC
1 TCCGTGCCTAAAATTCAGGCACTGGCATAAGC
*
19281 TCCGTGCCTAAAATTTAGGCACGTGGCATA
1 TCCGTGCCTAAAATTCAGGCAC-TGGCATA
19311 TAGGAATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.72
33 7 0.28
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (32 bp):
TCCGTGCCTAAAATTCAGGCACTGGCATAAGC
Found at i:19396 original size:13 final size:13
Alignment explanation
Indices: 19378--19402 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19368 TCTACCTTTA
19378 ACTCCCGTGCCTG
1 ACTCCCGTGCCTG
19391 ACTCCCGTGCCT
1 ACTCCCGTGCCT
19403 AAATATGATT
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:0.08, C:0.48, G:0.20, T:0.24
Consensus pattern (13 bp):
ACTCCCGTGCCTG
Found at i:22562 original size:11 final size:11
Alignment explanation
Indices: 22519--22556 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22509 TTCCTATATA
*
22519 AAATAAATTAT
1 AAATTAATTAT
22530 CAAA-TAATTAT
1 -AAATTAATTAT
22541 AAATTAATTAT
1 AAATTAATTAT
22552 AAATT
1 AAATT
22557 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:22936 original size:28 final size:31
Alignment explanation
Indices: 22879--22939 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
22869 CAATATTTAT
* *
22879 TTTTTTGTGTATTATTAGTATGTAACATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
22910 TTTTTTGTGTATTA-TAATA-ATAA-ATTAA
1 TTTTTTGTGTATTATTAATATATAACATTAA
22938 TT
1 TT
22940 ATAGTTTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTGTGTATTATTAATATATAACATTAA
Found at i:23089 original size:11 final size:11
Alignment explanation
Indices: 23065--23104 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
23055 AAAACAATTC
23065 TATAAAATAAT
1 TATAAAATAAT
* *
23076 TATCAAATACT
1 TATAAAATAAT
23087 TATAAAATTAAT
1 TATAAAA-TAAT
23099 TATAAA
1 TATAAA
23105 TTTCATTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:24284 original size:30 final size:30
Alignment explanation
Indices: 24248--24304 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
24238 ATTAATTGAG
*
24248 TTTTTTTCGACCTTATTAAACTTTTTACCT
1 TTTTTTTCGACCTTATAAAACTTTTTACCT
* * *
24278 TTTTTTTTGGCCTTATAAAATTTTTTA
1 TTTTTTTCGACCTTATAAAACTTTTTA
24305 GTCACCTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTTTTTCGACCTTATAAAACTTTTTACCT
Found at i:24782 original size:25 final size:25
Alignment explanation
Indices: 24748--24796 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
24738 CCAAACAATC
24748 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
24773 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
24797 CAAATCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:25150 original size:7 final size:7
Alignment explanation
Indices: 25117--25141 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25107 AATTCCATCA
25117 AATCTTC
1 AATCTTC
25124 AATCTTC
1 AATCTTC
25131 AATCTTC
1 AATCTTC
25138 AATC
1 AATC
25142 AATCTTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
AATCTTC
Found at i:25709 original size:25 final size:25
Alignment explanation
Indices: 25675--25723 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
25665 CCAAACAATC
25675 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
25700 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
25724 CAAATCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:26374 original size:86 final size:90
Alignment explanation
Indices: 26269--26436 Score: 263
Period size: 86 Copynumber: 1.9 Consensus size: 90
26259 ACCTTGTAAA
* *
26269 TTTTCTTGGTAAGCCTATAAATTTTTCATCAAACTTAAAACCTTTTTAAATA-GTTT-T-CTTAA
1 TTTTCTTGATAAGCCTATAAATTTTTCATCAAACTTAAAACCTTTTTAAATAGGTTTCTAATTAA
26331 ATTTATTCAATCACCTCGTTTAAGC
66 ATTTATTCAATCACCTCGTTTAAGC
* * *
26356 TTTT-TTGATAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTTTTAAATAGGTTTCTAATTAA
1 TTTTCTTGATAAGCCTATAAATTTTTCATCAAACTTAAAACCTTTTTAAATAGGTTTCTAATTAA
26420 ATTTATTCAATCACCTC
66 ATTTATTCAATCACCTC
26437 ATTTTAAAGA
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
86 43 0.59
87 8 0.11
88 1 0.01
89 21 0.29
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (90 bp):
TTTTCTTGATAAGCCTATAAATTTTTCATCAAACTTAAAACCTTTTTAAATAGGTTTCTAATTAA
ATTTATTCAATCACCTCGTTTAAGC
Found at i:26551 original size:20 final size:21
Alignment explanation
Indices: 26517--26574 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
26507 CCTTGTAAGA
26517 TTTATAGTTAA-CTTATGAA-T
1 TTTATAG-TAACCTTATGAAGT
*
26537 TTTATAGTAACCTTAAGAAGTT
1 TTTATAGTAACCTTATGAAG-T
*
26559 TTTTTAGTAACCTTAT
1 TTTATAGTAACCTTAT
26575 TGAGTGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
22 15 0.47
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (21 bp):
TTTATAGTAACCTTATGAAGT
Found at i:31512 original size:67 final size:68
Alignment explanation
Indices: 31423--31560 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 68
31413 GTGATAATTT
*
31423 TTAGGGGAAAAAAAATTTCGATGAGGAGAGGGAAGAAGG-AAAAAAAATTGCTGTTAAGCAATAG
1 TTAGGGGAAAAAAAATTTCGATGAGGAGAAGGAAGAAGGAAAAAAAAATTGCTGTTAAGCAATAG
31487 CTC
66 CTC
* *
31490 TTAGAGGGAAAAAAAA-TTCGATGAGGAGAAGGAAGAAGGAAAAAAAAAATTGTTGTTAGGCAAT
1 TTAG-GGGAAAAAAAATTTCGATGAGGAGAAGGAAGAAGG-AAAAAAAAATTGCTGTTAAGCAAT
31554 AGCTC
64 AGCTC
31559 TT
1 TT
31561 GATACCATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
67 26 0.40
68 11 0.17
69 28 0.43
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.20
Consensus pattern (68 bp):
TTAGGGGAAAAAAAATTTCGATGAGGAGAAGGAAGAAGGAAAAAAAAATTGCTGTTAAGCAATAG
CTC
Found at i:31702 original size:25 final size:23
Alignment explanation
Indices: 31673--31724 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
31663 CATTGGTTAC
*
31673 ATTTAAGTTTAAAACTAATAACATG
1 ATTTAAATTT-AAACTAATAACA-G
* *
31698 ATTTAAATTTGAACTAGTAACAG
1 ATTTAAATTTAAACTAATAACAG
31721 ATTT
1 ATTT
31725 GATAAGGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 10 0.42
25 9 0.38
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (23 bp):
ATTTAAATTTAAACTAATAACAG
Found at i:31750 original size:30 final size:30
Alignment explanation
Indices: 31716--31786 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
31706 TTGAACTAGT
31716 AACAGATTTGATAAGGCTTAGGTTCAAACC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
31746 AACAGATTTGATAAGGCTTAGGTTCAAACC
1 AACAGATTTGATAAGGCTTAGGTTCAAACC
31776 AA-AGGATTTGA
1 AACA-GATTTGA
31787 ACAATTCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 1 0.03
30 39 0.98
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (30 bp):
AACAGATTTGATAAGGCTTAGGTTCAAACC
Found at i:34068 original size:15 final size:15
Alignment explanation
Indices: 34048--34078 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34038 ACCAAAAGAA
*
34048 TCATTGTGATACTTC
1 TCATTGTCATACTTC
34063 TCATTGTCATACTTC
1 TCATTGTCATACTTC
34078 T
1 T
34079 TCACAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (15 bp):
TCATTGTCATACTTC
Found at i:34561 original size:41 final size:43
Alignment explanation
Indices: 34504--34584 Score: 148
Period size: 41 Copynumber: 1.9 Consensus size: 43
34494 CTGATGTCAA
34504 AAGCATATCATTCAAGA-TTTTTTTTACCT-AAAAAAAAACAT
1 AAGCATATCATTCAAGATTTTTTTTTACCTCAAAAAAAAACAT
34545 AAGCATATCATTCAAGATTTTTTTTTACCTCAAAAAAAAA
1 AAGCATATCATTCAAGATTTTTTTTTACCTCAAAAAAAAA
34585 AAAAACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 17 0.45
42 12 0.32
43 9 0.24
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.35
Consensus pattern (43 bp):
AAGCATATCATTCAAGATTTTTTTTTACCTCAAAAAAAAACAT
Found at i:34856 original size:19 final size:17
Alignment explanation
Indices: 34820--34860 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
34810 TTCTTTGTTT
*
34820 GAAAACAAAAAAGGAAA
1 GAAAACAAAAAAGAAAA
34837 GAAAACAAAAAAAGCAAAA
1 GAAAAC-AAAAAAG-AAAA
34856 GAAAA
1 GAAAA
34861 TCAACCGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 8 0.38
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (17 bp):
GAAAACAAAAAAGAAAA
Found at i:35120 original size:7 final size:7
Alignment explanation
Indices: 35100--35132 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
35090 TCATCTTCTT
35100 TCCAGAC
1 TCCAGAC
35107 T-CAGAC
1 TCCAGAC
35113 TCCAGAC
1 TCCAGAC
35120 TCCAGAC
1 TCCAGAC
35127 TCCAGA
1 TCCAGA
35133 GCCCTTGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.15
Consensus pattern (7 bp):
TCCAGAC
Found at i:38949 original size:81 final size:82
Alignment explanation
Indices: 38814--38978 Score: 260
Period size: 81 Copynumber: 2.0 Consensus size: 82
38804 TTGAATTCTC
* * *
38814 CTGTTATTGCAATAGACCTACCTTCAATTTCTTACAGTTCGTCTTGAGGAAATGAGG-ATCAATC
1 CTGTTATTGAAACAGACCTACCTTCAATCTCTTACAGTTCGTCTTGAGGAAATGAGGAATCAATC
*
38878 TCTTCTATAATCATGGT
66 TCTTATATAATCATGGT
38895 CTGTTATTGAAACAGACCTACCTTCAATCTCTTACAGTTCGTCTTGAGGAAATGAGGATCATCAA
1 CTGTTATTGAAACAGACCTACCTTCAATCTCTTACAGTTCGTCTTGAGGAAATGAGGA--ATCAA
*
38960 TCTCTTATATGATCATGGT
64 TCTCTTATATAATCATGGT
38979 TTATATAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 54 0.71
84 22 0.29
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (82 bp):
CTGTTATTGAAACAGACCTACCTTCAATCTCTTACAGTTCGTCTTGAGGAAATGAGGAATCAATC
TCTTATATAATCATGGT
Done.