Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018457.1 Corchorus olitorius cultivar O-4 contig18490, 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: 46414
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--37 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA
3 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38 CTACATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:311 original size:56 final size:57
Alignment explanation
Indices: 221--335 Score: 196
Period size: 56 Copynumber: 2.0 Consensus size: 57
211 TATTCGTTTC
221 CTTTCACACAATAAATGTTATAATAAATCATATCCCC-CTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCTCTATCTCTACTTAATTATT
* * *
277 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCTTTATCTCTATTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCTCTATCTCTACTTAATTATT
334 CT
1 CT
336 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 36 0.65
57 19 0.35
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.42
Consensus pattern (57 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCTCTATCTCTACTTAATTATT
Found at i:460 original size:42 final size:42
Alignment explanation
Indices: 401--481 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
391 TAAGGATCAA
401 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
443 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
482 AAGATTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:10753 original size:20 final size:20
Alignment explanation
Indices: 10728--10778 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
10718 TTTTATGAAA
10728 TTTGATAAT-CACTATAAAAT
1 TTTGATAATCCA-TATAAAAT
10748 TTTGATAACCTCCATATAAAAT
1 TTTGATAA--TCCATATAAAAT
*
10770 TTTAATAAT
1 TTTGATAAT
10779 TACATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (20 bp):
TTTGATAATCCATATAAAAT
Found at i:10768 original size:22 final size:22
Alignment explanation
Indices: 10740--10861 Score: 70
Period size: 22 Copynumber: 5.5 Consensus size: 22
10730 TGATAATCAC
10740 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* * *
10762 TATAAAATTTTAATAA-TTACA
1 TATAAAATTTTGATAACCTCCA
* * * * *
10783 TTATAAAGTTTTTATGACGATAC-
1 -TATAAAATTTTGATAAC-CTCCA
* *
10806 TATAAAATTTCGAGAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* * *
10828 TATGAAATTTTGTTAACTTTCC-
1 TATAAAATTTTGATAAC-CTCCA
*
10850 TGTAAAATTTTG
1 TATAAAATTTTG
10862 TTACACTTTT
Statistics
Matches: 74, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
21 5 0.07
22 63 0.85
23 3 0.04
24 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCA
Found at i:11018 original size:22 final size:20
Alignment explanation
Indices: 10993--11237 Score: 171
Period size: 22 Copynumber: 11.8 Consensus size: 20
10983 TATTCACATT
10993 ATGAAATTTTGATAACCATACC
1 ATGAAATTTTGATAACC-T-CC
*
11015 ATGAAATTGTGAT-ACCTCAC
1 ATGAAATTTTGATAACCTC-C
11035 TATGAAATTTT-ATAAACCTCCCC
1 -ATGAAATTTTGAT-AACCT--CC
*
11058 ATAAAATTTTGATAACCT-C
1 ATGAAATTTTGATAACCTCC
* *
11077 ATGAAATTTTGAAAACCACCTC
1 ATGAAATTTTGATAACC-TC-C
*
11099 ATGAAATTTTGATAACCATCTT
1 ATGAAATTTTGATAACC-TC-C
*
11121 ATGAAATTTTGATAACATCCC
1 ATGAAATTTTGATAACCT-CC
*
11142 TAT-AAATTTTTTATAACCT-C
1 -ATGAAA-TTTTGATAACCTCC
* *
11162 ATAAAATTTTGTTAACCTCC
1 ATGAAATTTTGATAACCTCC
**
11182 TACAAAATTTTGATAACACT--
1 -ATGAAATTTTGATAAC-CTCC
* *
11202 ATTAAATTTTGATAACCCCC
1 ATGAAATTTTGATAACCTCC
11222 AATGAAATTTTGATAA
1 -ATGAAATTTTGATAA
11238 TTAATTACAC
Statistics
Matches: 182, Mismatches: 21, Indels: 41
0.75 0.09 0.17
Matches are distributed among these distances:
18 1 0.01
19 43 0.24
20 9 0.05
21 44 0.24
22 81 0.45
23 3 0.02
24 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (20 bp):
ATGAAATTTTGATAACCTCC
Found at i:11093 original size:41 final size:41
Alignment explanation
Indices: 10993--11237 Score: 205
Period size: 41 Copynumber: 5.9 Consensus size: 41
10983 TATTCACATT
* * *
10993 ATGAAATTTTGATAACCAT-ACCATGAAATTGTGAT-ACCTCAC
1 ATGAAATTTTGATAACC-TCCCCATAAAATTTTGATAACCT--C
11035 TATGAAATTTT-ATAAACCTCCCCATAAAATTTTGATAACCTC
1 -ATGAAATTTTGAT-AACCTCCCCATAAAATTTTGATAACCTC
* * * *
11077 ATGAAATTTTGAAAACCACCTCATGAAATTTTGATAACCATC
1 ATGAAATTTTGATAACCTCCCCATAAAATTTTGATAACC-TC
* * * *
11119 TTATGAAATTTTGATAACATCCCTATAAATTTTTTATAACCTC
1 --ATGAAATTTTGATAACCTCCCCATAAAATTTTGATAACCTC
* * * *
11162 ATAAAATTTTGTTAACCT-CCTACAAAATTTTGATAACACT-
1 ATGAAATTTTGATAACCTCCCCATAAAATTTTGATAAC-CTC
* * *
11202 ATTAAATTTTGATAACC-CCCAATGAAATTTTGATAA
1 ATGAAATTTTGATAACCTCCCCATAAAATTTTGATAA
11238 TTAATTACAC
Statistics
Matches: 167, Mismatches: 26, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
40 46 0.28
41 50 0.30
42 7 0.04
43 29 0.17
44 35 0.21
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (41 bp):
ATGAAATTTTGATAACCTCCCCATAAAATTTTGATAACCTC
Found at i:11148 original size:21 final size:22
Alignment explanation
Indices: 10992--11367 Score: 143
Period size: 22 Copynumber: 17.5 Consensus size: 22
10982 GTATTCACAT
*
10992 TATGAAATTTTGATAACCATACC
1 TATGAAATTTTGATAA-CATCCC
* * *
11015 -ATGAAATTGTGAT-ACCTCAC
1 TATGAAATTTTGATAACATCCC
*
11035 TATGAAATTTT-ATAAACCTCCC
1 TATGAAATTTTGAT-AACATCCC
* * *
11057 CATAAAATTTTGATAAC--CTC
1 TATGAAATTTTGATAACATCCC
*
11077 -ATGAAATTTTGA-AA-ACCACC
1 TATGAAATTTTGATAACATC-CC
*
11097 TCATGAAATTTTGATAACCAT-CT
1 T-ATGAAATTTTGATAA-CATCCC
11120 TATGAAATTTTGATAACATCCC
1 TATGAAATTTTGATAACATCCC
* *
11142 TAT-AAATTTTTTATAAC--CTC
1 TATGAAA-TTTTGATAACATCCC
* * *
11162 -ATAAAATTTTGTTAACCT-CC
1 TATGAAATTTTGATAACATCCC
**
11182 TACAAAATTTTGATAACA---C
1 TATGAAATTTTGATAACATCCC
* *
11201 TATTAAATTTTGATAAC-CCCC
1 TATGAAATTTTGATAACATCCC
* *
11222 AATGAAATTTTGATAATTAATTACACC
1 TATGAAATTTTGATAA--CA-T-C-CC
* *
11249 -ATGAAATTATT-ATAACTTACC
1 TATGAAATT-TTGATAACATCCC
*
11270 TATGAAATTTTGTTAATC-TCCC
1 TATGAAATTTTGATAA-CATCCC
* * * *
11292 TATAAAATTTTAAGAACCA-CAC
1 TATGAAATTTTGATAA-CATCCC
* * *
11314 TATCAAATTTTGTTAATC-TCAC
1 TATGAAATTTTGATAA-CATCCC
* **
11336 TAT-AAATTTTGATAAAATCAT
1 TATGAAATTTTGATAACATCCC
11357 TATGAAATTTT
1 TATGAAATTTT
11368 AACTACCACA
Statistics
Matches: 271, Mismatches: 47, Indels: 71
0.70 0.12 0.18
Matches are distributed among these distances:
18 2 0.01
19 38 0.14
20 14 0.05
21 66 0.24
22 125 0.46
23 8 0.03
25 1 0.00
26 13 0.05
27 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACATCCC
Found at i:11437 original size:61 final size:60
Alignment explanation
Indices: 11354--11470 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 60
11344 TTGATAAAAT
* *
11354 CATTATGAAATTTTAACTACCACAC-AGTGAAAATTTGATAATCTCTCCCTCTGAAATACCA
1 CATTATAAAATTTTAACTACCACACTA-TGAAAATTTGATAATCTC-CCCTCTAAAATACCA
* *
11415 CATTATAAAATTTTGA-TAACCACACTATGAAATTTTGATAATCTCCCCTCTAAAAT
1 CATTATAAAATTTTAACT-ACCACACTATGAAAATTTGATAATCTCCCCTCTAAAAT
11471 TCCGATAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
60 11 0.22
61 38 0.76
62 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (60 bp):
CATTATAAAATTTTAACTACCACACTATGAAAATTTGATAATCTCCCCTCTAAAATACCA
Found at i:11447 original size:22 final size:22
Alignment explanation
Indices: 11411--11455 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
11401 CCTCTGAAAT
*
11411 ACCACATTATAAAATTTTGATA
1 ACCACACTATAAAATTTTGATA
*
11433 ACCACACTATGAAATTTTGATA
1 ACCACACTATAAAATTTTGATA
11455 A
1 A
11456 TCTCCCCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (22 bp):
ACCACACTATAAAATTTTGATA
Found at i:11501 original size:22 final size:22
Alignment explanation
Indices: 11422--11504 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
11412 CCACATTATA
* * *
11422 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCTCCCCATG
* * *
11444 AAATTTTGATAATCTCCCCTCTA
1 AAATTTTGATAACCTCCCC-ATG
**
11467 AAATTCCGATAACCTCCCCATG
1 AAATTTTGATAACCTCCCCATG
*
11489 AAATTTTGTTAACCTC
1 AAATTTTGATAACCTC
11505 TATGGAATTG
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
22 29 0.63
23 17 0.37
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCCATG
Found at i:11552 original size:18 final size:19
Alignment explanation
Indices: 11523--11560 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
11513 TGTGATTATT
11523 ACACTATGAAATTTTGGTA
1 ACACTATGAAATTTTGGTA
11542 ACACT-TGAAATTTTGGTA
1 ACACTATGAAATTTTGGTA
11560 A
1 A
11561 GCTCACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
ACACTATGAAATTTTGGTA
Found at i:11691 original size:22 final size:22
Alignment explanation
Indices: 11666--11713 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11656 TAACCAGAGT
11666 ATGAAATTTTAG-CAACCTCCCC
1 ATGAAATTTT-GCCAACCTCCCC
*
11688 ATGAAATTTTGCCAACCTTCCC
1 ATGAAATTTTGCCAACCTCCCC
11710 ATGA
1 ATGA
11714 TTTTCGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (22 bp):
ATGAAATTTTGCCAACCTCCCC
Found at i:11817 original size:44 final size:44
Alignment explanation
Indices: 11755--11870 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 44
11745 ACATCCCATG
* * * *
11755 AAATTGTGATAACTACACTATGAATTTTTAACATACTAC-CTATA
1 AAATTTTGGTAACCACACTATGAATTTTTAACA-ACCACACTATA
* ** * * *
11799 AAATTTTGGTAACCACACTATAAAAATTTGAGAACCGCACTATA
1 AAATTTTGGTAACCACACTATGAATTTTTAACAACCACACTATA
* *
11843 AAATTTTAGTAACCACACAATGAATTTT
1 AAATTTTGGTAACCACACTATGAATTTT
11871 GATAACTTCC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
43 3 0.05
44 53 0.95
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (44 bp):
AAATTTTGGTAACCACACTATGAATTTTTAACAACCACACTATA
Found at i:11819 original size:22 final size:22
Alignment explanation
Indices: 11794--11860 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
11784 AACATACTAC
11794 CTATAAAATTTTGGTAACCACA
1 CTATAAAATTTTGGTAACCACA
* *
11816 CTATAAAAATTTGAG-AACCGCA
1 CTATAAAATTTTG-GTAACCACA
*
11838 CTATAAAATTTTAGTAACCACA
1 CTATAAAATTTTGGTAACCACA
11860 C
1 C
11861 AATGAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.28
Consensus pattern (22 bp):
CTATAAAATTTTGGTAACCACA
Found at i:13160 original size:45 final size:45
Alignment explanation
Indices: 13109--13196 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
13099 CCTAAATTTA
*
13109 ACTCCTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCT
1 ACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCT
* *
13154 ACTCCTCCATCTCTATATAATTCATCAAAATAAAGTTAATATT
1 ACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
13197 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (45 bp):
ACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCT
Found at i:13868 original size:12 final size:12
Alignment explanation
Indices: 13851--13878 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13841 GAATTAAAAG
13851 TTATTTTTTATT
1 TTATTTTTTATT
13863 TTATTTTTTATT
1 TTATTTTTTATT
13875 TTAT
1 TTAT
13879 GTTAGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:14976 original size:150 final size:151
Alignment explanation
Indices: 14759--15065 Score: 510
Period size: 150 Copynumber: 2.0 Consensus size: 151
14749 GGTCAATCAC
* * * * *
14759 AATAACCTTTTAAATTAAAATGGTAAAAAATAAAATAATTATAAAAATATTGAATTTAATTATAT
1 AATAAACTTTTAAATTAAAATAGTAAAAAATAAAATAATTATAAAAACATTAAATTTAATTAAAT
*
14824 GAAAATAGAGTTTTTAGTAAAATAAAACTGTATATT-AAAATTTTTAATATATCAAAGTTTTGAA
66 GAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAAAATTTTAATATATCAAAGTTTT-AA
14888 TGAAAAATAGTAAAATGGTAAA
130 TGAAAAATAGTAAAATGGTAAA
*
14910 AATAAACTTTTAAGTTAAAATAGT-AAAAATAAAATAATTATAAAAACATTAAATTTAATTAAAT
1 AATAAACTTTTAAATTAAAATAGTAAAAAATAAAATAATTATAAAAACATTAAATTTAATTAAAT
* *
14974 GAAAATAGAGTTTTTAGTAGAATAAAACTGTATATTAAAAAATTTTAATATATCTAAGTTTTAAT
66 GAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAAAATTTTAATATATCAAAGTTTTAAT
15039 GAAAAATAGTAAAATGGTAAA
131 GAAAAATAGTAAAATGGTAAA
15060 AATAAA
1 AATAAA
15066 GTAATTATAA
Statistics
Matches: 146, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
150 102 0.70
151 44 0.30
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.35
Consensus pattern (151 bp):
AATAAACTTTTAAATTAAAATAGTAAAAAATAAAATAATTATAAAAACATTAAATTTAATTAAAT
GAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAAAATTTTAATATATCAAAGTTTTAAT
GAAAAATAGTAAAATGGTAAA
Found at i:20490 original size:39 final size:39
Alignment explanation
Indices: 20410--20490 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
20400 ACCTCCTGCC
* *
20410 CCTTCTAAGCAGCAATCACCGCCACCGTCATCACCTCCT
1 CCTTCTAAGCAGCAATCACCGCCACCGTCACCAACTCCT
* *
20449 CCTTCTAAGCAGCAATCGCCGCCACCTTCAACCAACT-CT
1 CCTTCTAAGCAGCAATCACCGCCACCGTC-ACCAACTCCT
20488 CCT
1 CCT
20491 CCGGATTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 32 0.86
40 5 0.14
ACGTcount: A:0.23, C:0.46, G:0.10, T:0.21
Consensus pattern (39 bp):
CCTTCTAAGCAGCAATCACCGCCACCGTCACCAACTCCT
Found at i:32371 original size:39 final size:37
Alignment explanation
Indices: 32285--32379 Score: 117
Period size: 33 Copynumber: 2.6 Consensus size: 37
32275 ACGGTCACCG
* *
32285 CCATTTCCTGGCATTCTAATTCCCGGAGGAATCCCAT
1 CCATCTCCAGGCATTCTAATTCCCGGAGGAATCCCAT
*
32322 ---TC-CCAGGCATTCTAATTCCCGGAGGATTCCCAT
1 CCATCTCCAGGCATTCTAATTCCCGGAGGAATCCCAT
32355 GCCCATCTCCAGGCATTCTAATTCC
1 --CCATCTCCAGGCATTCTAATTCC
32380 TGCAGGTTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
33 29 0.59
34 1 0.02
38 2 0.04
39 17 0.35
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (37 bp):
CCATCTCCAGGCATTCTAATTCCCGGAGGAATCCCAT
Found at i:35218 original size:36 final size:36
Alignment explanation
Indices: 35171--35242 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
35161 TTATGGGATC
35171 AGCAGATTATTGATTAATAGGGGTGGGATCGCACTG
1 AGCAGATTATTGATTAATAGGGGTGGGATCGCACTG
35207 AGCAGATTATTGATTAATAGGGGTGGGATCGCACTG
1 AGCAGATTATTGATTAATAGGGGTGGGATCGCACTG
35243 CCTCCTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (36 bp):
AGCAGATTATTGATTAATAGGGGTGGGATCGCACTG
Found at i:41220 original size:3 final size:3
Alignment explanation
Indices: 41212--41278 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
41202 GTTCATTTCC
41212 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
41260 TCT TCT TCT TCT TTT TCT T
1 TCT TCT TCT TCT TCT TCT T
41279 TCTTTCTTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:41282 original size:4 final size:4
Alignment explanation
Indices: 41273--41299 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41263 TCTTCTTCTT
41273 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
41300 TTTATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:44646 original size:64 final size:64
Alignment explanation
Indices: 44545--44670 Score: 252
Period size: 64 Copynumber: 2.0 Consensus size: 64
44535 GGCTTGTTGA
44545 TATATCAGAGGACTGAGGGATATATATGGTGTCAACCTGTTACTTTTCGATCGCCAGATGCTGT
1 TATATCAGAGGACTGAGGGATATATATGGTGTCAACCTGTTACTTTTCGATCGCCAGATGCTGT
44609 TATATCAGAGGACTGAGGGATATATATGGTGTCAACCTGTTACTTTTCGATCGCCAGATGCT
1 TATATCAGAGGACTGAGGGATATATATGGTGTCAACCTGTTACTTTTCGATCGCCAGATGCT
44671 AATTACTGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (64 bp):
TATATCAGAGGACTGAGGGATATATATGGTGTCAACCTGTTACTTTTCGATCGCCAGATGCTGT
Found at i:45309 original size:15 final size:15
Alignment explanation
Indices: 45289--45318 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45279 ATCAGGCTGC
*
45289 CACGATACACGATAT
1 CACGATACACAATAT
45304 CACGATACACAATAT
1 CACGATACACAATAT
45319 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Done.