Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014972.1 Corchorus capsularis cultivar CVL-1 contig14993, 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: 80821
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:450 original size:31 final size:31
Alignment explanation
Indices: 382--548 Score: 136
Period size: 31 Copynumber: 5.3 Consensus size: 31
372 ACGGCGTCCG
* * * **
382 ACGTGACATGCCACGTGTCATTTTTTGAAAC
1 ACGTGGCATGCCACATGTCACTTTTTGGTAC
* * *
413 ATGTGGCATGTCACGTGTCACTTTTTGGTAC
1 ACGTGGCATGCCACATGTCACTTTTTGGTAC
* ** *
444 ACGTGGCGTGATATATGTCACTTTTTTGGTAC
1 ACGTGGCATGCCACATGTCAC-TTTTTGGTAC
* * * *
476 ATGTTGCGTGCCGCATGTCACTTTTTGGTAC
1 ACGTGGCATGCCACATGTCACTTTTTGGTAC
* * * *
507 ACGTGGCGTGCCGCATGTCACTTTTTTTGTAT
1 ACGTGGCATGCCACATGTCAC-TTTTTGGTAC
539 ACGTGGCATG
1 ACGTGGCATG
549 TCACGTCAGA
Statistics
Matches: 111, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
31 69 0.62
32 42 0.38
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.37
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTCACTTTTTGGTAC
Found at i:475 original size:32 final size:31
Alignment explanation
Indices: 428--532 Score: 147
Period size: 31 Copynumber: 3.4 Consensus size: 31
418 GCATGTCACG
****
428 TGTCACTTTTTGGTACACGTGGCGTGATATA
1 TGTCACTTTTTGGTACACGTGGCGTGCCGCA
* *
459 TGTCACTTTTTTGGTACATGTTGCGTGCCGCA
1 TGTCAC-TTTTTGGTACACGTGGCGTGCCGCA
491 TGTCACTTTTTGGTACACGTGGCGTGCCGCA
1 TGTCACTTTTTGGTACACGTGGCGTGCCGCA
522 TGTCACTTTTT
1 TGTCACTTTTT
533 TTGTATACGT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
31 40 0.62
32 25 0.38
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (31 bp):
TGTCACTTTTTGGTACACGTGGCGTGCCGCA
Found at i:543 original size:32 final size:32
Alignment explanation
Indices: 428--545 Score: 150
Period size: 32 Copynumber: 3.8 Consensus size: 32
418 GCATGTCACG
****
428 TGTCAC-TTTTTGGTACACGTGGCGTGATATA
1 TGTCACTTTTTTGGTACACGTGGCGTGCCGCA
* *
459 TGTCACTTTTTTGGTACATGTTGCGTGCCGCA
1 TGTCACTTTTTTGGTACACGTGGCGTGCCGCA
491 TGTCAC-TTTTTGGTACACGTGGCGTGCCGCA
1 TGTCACTTTTTTGGTACACGTGGCGTGCCGCA
* *
522 TGTCACTTTTTTTGTATACGTGGC
1 TGTCACTTTTTTGGTACACGTGGC
546 ATGTCACGTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
31 35 0.47
32 40 0.53
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.40
Consensus pattern (32 bp):
TGTCACTTTTTTGGTACACGTGGCGTGCCGCA
Found at i:2222 original size:10 final size:10
Alignment explanation
Indices: 2200--2238 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
2190 AAATCTCGAT
*
2200 ATATCCGTAA
1 ATATCCATAA
2210 ATATCCATAA
1 ATATCCATAA
**
2220 ATATCTGTAA
1 ATATCCATAA
2230 ATATCCATA
1 ATATCCATA
2239 TTAAATTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (10 bp):
ATATCCATAA
Found at i:2223 original size:20 final size:20
Alignment explanation
Indices: 2200--2238 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2190 AAATCTCGAT
2200 ATATCCGTAAATATCCATAA
1 ATATCCGTAAATATCCATAA
*
2220 ATATCTGTAAATATCCATA
1 ATATCCGTAAATATCCATA
2239 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATCCGTAAATATCCATAA
Found at i:3287 original size:13 final size:12
Alignment explanation
Indices: 3257--3299 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
3247 CATCGATACC
3257 TCGATATATCCG
1 TCGATATATCCG
3269 TCGATATATCCG
1 TCGATATATCCG
3281 TTCGATATATCCG
1 -TCGATATATCCG
3294 TCGATA
1 TCGATA
3300 CCTGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:8164 original size:2 final size:2
Alignment explanation
Indices: 8157--8187 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8147 ATGAAATAGT
8157 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 T
8188 TGATTGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14742 original size:99 final size:102
Alignment explanation
Indices: 14558--14746 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 102
14548 CCTATGAGTG
* * *
14558 CCTCCCAACAAGCAAATATTAGCAGTTTGTCATCACAGTCACACAATGGTGCAAGTGTTCGGAAG
1 CCTCCCAACAAGCAAATACTAGCAGTTTGTCAT-ACA-T-ACACAATGGTGCAAATGTTCAGAAG
14623 CAAAACATGAATACTCTTCAGTCAATTGTTGCAAGTAGTA
63 CAAAACATGAATACTCTTCAGTCAATTGTTGCAAGTAGTA
* * * * *
14663 CCTCCCAGCAAGCAAATACTAGCAGTTTGTCAT-C-T-CAGAGTGGTGTAAATGTTCAGCAGCAA
1 CCTCCCAACAAGCAAATACTAGCAGTTTGTCATACATACACAATGGTGCAAATGTTCAGAAGCAA
*
14725 AACATGAATCCTCTTCAGTCAA
66 AACATGAATACTCTTCAGTCAA
14747 ATCTCTACGA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
99 42 0.56
101 1 0.01
103 1 0.01
105 31 0.41
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (102 bp):
CCTCCCAACAAGCAAATACTAGCAGTTTGTCATACATACACAATGGTGCAAATGTTCAGAAGCAA
AACATGAATACTCTTCAGTCAATTGTTGCAAGTAGTA
Found at i:14985 original size:18 final size:18
Alignment explanation
Indices: 14884--14981 Score: 124
Period size: 18 Copynumber: 5.4 Consensus size: 18
14874 ACAAGAGTTT
*
14884 CAGACGCACCATATGCCA
1 CAGACGCACCAGATGCCA
* *
14902 CAGACGCAGCAGATGCAA
1 CAGACGCACCAGATGCCA
14920 CAGACGCACCAGATGCCA
1 CAGACGCACCAGATGCCA
* *
14938 CAGAGGCACCAGATACCA
1 CAGACGCACCAGATGCCA
* * *
14956 CATATGCAGCAGATGCCA
1 CAGACGCACCAGATGCCA
14974 CAGACGCA
1 CAGACGCA
14982 GCAGCATCAG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.36, C:0.34, G:0.22, T:0.08
Consensus pattern (18 bp):
CAGACGCACCAGATGCCA
Found at i:19816 original size:2 final size:2
Alignment explanation
Indices: 19759--19798 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
19749 CTTTTTAGTA
19759 AT AT CAT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19799 GCCAATGTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23908 original size:27 final size:27
Alignment explanation
Indices: 23870--23926 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
23860 GGTTATAAAT
23870 CTCCCCTTCAAGTTCAAATTCATCAAA
1 CTCCCCTTCAAGTTCAAATTCATCAAA
23897 CTCCCCTTCAAGTTCAAATTCATCAAA
1 CTCCCCTTCAAGTTCAAATTCATCAAA
23924 CTC
1 CTC
23927 ACCAATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.30
Consensus pattern (27 bp):
CTCCCCTTCAAGTTCAAATTCATCAAA
Found at i:27439 original size:99 final size:99
Alignment explanation
Indices: 27264--27457 Score: 343
Period size: 99 Copynumber: 2.0 Consensus size: 99
27254 TGCAAGAATG
* * *
27264 GCAAATGCTGCAGTCACAAAGTCAACAGCGCCAGATGCAATCACAACAGTATCACCAGCAAGTGA
1 GCAAATCCTGCAGTCACAAAGTCAACAGCCCCAGATGCAATCACAACAGTATCACCAGCAAGTAA
*
27329 AGCAAGTGTTTCCTACACAAGAGTTTCAGACGCA
66 AGCAAGAGTTTCCTACACAAGAGTTTCAGACGCA
*
27363 GCAAATCCTGCAGTCGCAAAGTCAACAGCCCCAGATGCAATCACAACAGTATCACCAGCAAGTAA
1 GCAAATCCTGCAGTCACAAAGTCAACAGCCCCAGATGCAATCACAACAGTATCACCAGCAAGTAA
27428 AGCAAGAGTTTCCTACACAAGAGTTTCAGA
66 AGCAAGAGTTTCCTACACAAGAGTTTCAGA
27458 TGCACCAGAT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 90 1.00
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (99 bp):
GCAAATCCTGCAGTCACAAAGTCAACAGCCCCAGATGCAATCACAACAGTATCACCAGCAAGTAA
AGCAAGAGTTTCCTACACAAGAGTTTCAGACGCA
Found at i:28535 original size:12 final size:12
Alignment explanation
Indices: 28518--28545 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28508 AATAAGATGC
28518 TATTTTCTTTCA
1 TATTTTCTTTCA
28530 TATTTTCTTTCA
1 TATTTTCTTTCA
28542 TATT
1 TATT
28546 GTTATATCCT
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:0.14, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTCTTTCA
Found at i:29028 original size:21 final size:21
Alignment explanation
Indices: 29003--29042 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28993 ATTTCTTTTC
29003 CAAAATTACTTTCTGATAACT
1 CAAAATTACTTTCTGATAACT
29024 CAAAATTACTTTCTGATAA
1 CAAAATTACTTTCTGATAA
29043 TATATAACGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (21 bp):
CAAAATTACTTTCTGATAACT
Found at i:29140 original size:24 final size:24
Alignment explanation
Indices: 29111--29270 Score: 146
Period size: 24 Copynumber: 6.3 Consensus size: 24
29101 AGATTTGATA
29111 AACTCAGCCAAGAGGAATTAGATG
1 AACTCAGCCAAGAGGAATTAGATG
29135 AACTCAGCCGAA-AGGAATTAGAT-
1 AACTCAGCC-AAGAGGAATTAGATG
* *
29158 AAGATCAGCCAAGAGGAATTAAATG
1 AA-CTCAGCCAAGAGGAATTAGATG
29183 AAGTCAGGCTCAGCCAAGAGGAATTAGATG
1 -A---A--CTCAGCCAAGAGGAATTAGATG
* *
29213 AACTCAGCCCATTTGAGGAATTAGAAG
1 AACTCAG-CCA--AGAGGAATTAGATG
*
29240 AACTCAGCCAAGA-GATATTAGATA
1 AACTCAGCCAAGAGGA-ATTAGATG
29264 AACTCAG
1 AACTCAG
29271 GTGGATATCT
Statistics
Matches: 114, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
23 6 0.05
24 56 0.49
25 5 0.04
26 5 0.04
27 19 0.17
29 2 0.02
30 21 0.18
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (24 bp):
AACTCAGCCAAGAGGAATTAGATG
Found at i:29198 original size:30 final size:30
Alignment explanation
Indices: 29162--29219 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
29152 TTAGATAAGA
*
29162 TCAGCCAAGAGGAATTAAATGAAGTCAGGC
1 TCAGCCAAGAGGAATTAAATGAACTCAGGC
*
29192 TCAGCCAAGAGGAATTAGATGAACTCAG
1 TCAGCCAAGAGGAATTAAATGAACTCAG
29220 CCCATTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (30 bp):
TCAGCCAAGAGGAATTAAATGAACTCAGGC
Found at i:29589 original size:3 final size:3
Alignment explanation
Indices: 29574--29623 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
29564 TGAGAAAATT
29574 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29619 ATA AT
1 ATA AT
29624 GTAATTATAG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:30309 original size:294 final size:294
Alignment explanation
Indices: 29780--30373 Score: 1143
Period size: 294 Copynumber: 2.0 Consensus size: 294
29770 TCCAATGTTC
29780 AGATATATCATATACTCAGAATGGGTAAATACAGTGCAAAGGTTAACCAACAAATTACTGTTTCT
1 AGATATATCATATACTCAGAATGGGTAAATACAGTGCAAAGGTTAACCAACAAATTACTGTTTCT
*
29845 TTCCTTAAGTCTTGGTCTTTCCAAACTTAATTATCAGCTGAAATTGGTTACTGTCAGATACCATA
66 TTCCTTAAGTCTTAGTCTTTCCAAACTTAATTATCAGCTGAAATTGGTTACTGTCAGATACCATA
*
29910 TGATATATCTGAACTGTCATATATTATATATAGGAGAAAAATGGAAAAAATATCCTATCATATCC
131 TGATATATCTAAACTGTCATATATTATATATAGGAGAAAAATGGAAAAAATATCCTATCATATCC
* *
29975 TGTAACATTTAACTGAAAATCAGAATCCCTTCTGTGTTACCATAGAAGATCAAACCCTGTCTGTT
196 CGTAACATTTAACTGAAAATCAGAATCCCTTCTGTGTTACCATAGAAGATCAAACCCTGTCTATT
30040 CCATTTTGGGAAGAACAGGCTAATACAAGACTGT
261 CCATTTTGGGAAGAACAGGCTAATACAAGACTGT
30074 AGATATATCATATACTCAGAATGGGTAAATACAGTGCAAAGGTTAACCAACAAATTACTGTTTCT
1 AGATATATCATATACTCAGAATGGGTAAATACAGTGCAAAGGTTAACCAACAAATTACTGTTTCT
30139 TTCCTTAAGTCTTAGTCTTTCCAAACTTAATTATCAGCTGAAATTGGTTACTGTCAGATACCATA
66 TTCCTTAAGTCTTAGTCTTTCCAAACTTAATTATCAGCTGAAATTGGTTACTGTCAGATACCATA
30204 TGATATATCTAAACTGTCATATATTATATATAGGAGAAAAATGGAAAAAATATCCTATCATATCC
131 TGATATATCTAAACTGTCATATATTATATATAGGAGAAAAATGGAAAAAATATCCTATCATATCC
*
30269 CGTAACATTTAACTGAAAATCAGAATCCCTTTTGTGTTACCATAGAAGATCAAACCCTGTCTATT
196 CGTAACATTTAACTGAAAATCAGAATCCCTTCTGTGTTACCATAGAAGATCAAACCCTGTCTATT
30334 CCATTTTGGGAAGAACAGGCTAATACAAGACTGT
261 CCATTTTGGGAAGAACAGGCTAATACAAGACTGT
30368 AGATAT
1 AGATAT
30374 TGTTTCTAGA
Statistics
Matches: 295, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
294 295 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (294 bp):
AGATATATCATATACTCAGAATGGGTAAATACAGTGCAAAGGTTAACCAACAAATTACTGTTTCT
TTCCTTAAGTCTTAGTCTTTCCAAACTTAATTATCAGCTGAAATTGGTTACTGTCAGATACCATA
TGATATATCTAAACTGTCATATATTATATATAGGAGAAAAATGGAAAAAATATCCTATCATATCC
CGTAACATTTAACTGAAAATCAGAATCCCTTCTGTGTTACCATAGAAGATCAAACCCTGTCTATT
CCATTTTGGGAAGAACAGGCTAATACAAGACTGT
Found at i:37138 original size:6 final size:6
Alignment explanation
Indices: 37127--37165 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
37117 AGGTGCTTCC
* * *
37127 GCAACA GCAACA GCAACA GCAGCA GCAGCA GCAGCA GCA
1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCA
37166 GCTATATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.41, C:0.33, G:0.26, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:37144 original size:12 final size:12
Alignment explanation
Indices: 37127--37165 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
37117 AGGTGCTTCC
*
37127 GCAACAGCAACA
1 GCAACAGCAGCA
37139 GCAACAGCAGCA
1 GCAACAGCAGCA
*
37151 GCAGCAGCAGCA
1 GCAACAGCAGCA
37163 GCA
1 GCA
37166 GCTATATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.33, G:0.26, T:0.00
Consensus pattern (12 bp):
GCAACAGCAGCA
Found at i:37151 original size:3 final size:3
Alignment explanation
Indices: 37131--37167 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
37121 GCTTCCGCAA
* *
37131 CAG CAA CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
37168 TATATCATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.35, G:0.27, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:37544 original size:3 final size:3
Alignment explanation
Indices: 37538--37581 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
37528 CTCCACCGTC
* * *
37538 GCA GCA GCA GCA GCA GCA GCA GCA ACA GCA GCA ACA GCA ACA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GC
37582 CACATATGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.39, C:0.34, G:0.27, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:38483 original size:29 final size:29
Alignment explanation
Indices: 38411--38492 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
38401 CTGGGTCTTC
* * *
38411 TTTGATTGTA-ATAAAATTCAGGGGCTTG
1 TTTGATTGCATATAAAATTTAGGGGATTG
38439 TTTGATTGCATATAAAATTTAGGGGATTG
1 TTTGATTGCATATAAAATTTAGGGGATTG
** * *
38468 TTTGATTTTATGTAAAATATAGGGG
1 TTTGATTGCATATAAAATTTAGGGG
38493 CATATTTGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 9 0.20
29 37 0.80
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.41
Consensus pattern (29 bp):
TTTGATTGCATATAAAATTTAGGGGATTG
Found at i:44023 original size:38 final size:38
Alignment explanation
Indices: 43979--44111 Score: 97
Period size: 38 Copynumber: 3.3 Consensus size: 38
43969 GGCTTCTCTT
43979 TATTCAATCAGACACAACTCGATTTTAAATCAATTGTC
1 TATTCAATCAGACACAACTCGATTTTAAATCAATTGTC
* * * ** *
44017 TATTCAATTA-ATGATAACTCGATCCTAAATTAATTAGAGCTTCTC
1 TATTCAATCAGA-CACAACTCGATTTTAAATCAATT---G----TC
* *
44062 TTTATTTAATCAGACACAATTCGATTTTAAATCAATTGTC
1 --TATTCAATCAGACACAACTCGATTTTAAATCAATTGTC
44102 TATTCAATCA
1 TATTCAATCA
44112 ATGACAATTC
Statistics
Matches: 69, Mismatches: 15, Indels: 22
0.65 0.14 0.21
Matches are distributed among these distances:
37 1 0.01
38 36 0.52
40 2 0.03
41 1 0.01
44 1 0.01
45 2 0.03
47 25 0.36
48 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (38 bp):
TATTCAATCAGACACAACTCGATTTTAAATCAATTGTC
Found at i:44115 original size:85 final size:85
Alignment explanation
Indices: 43970--44135 Score: 269
Period size: 85 Copynumber: 2.0 Consensus size: 85
43960 TTAATAGAGG
* *
43970 GCTTCTCTTTATTCAATCAGACACAACTCGATTTTAAATCAATTGTCTATTCAATTAATGATAAC
1 GCTTCTCTTTATTCAATCAGACACAACTCGATTTTAAATCAATTGTCTATTCAATCAATGACAAC
*
44035 TCGATCCTAAATTAATTAGA
66 TCAATCCTAAATTAATTAGA
* * *
44055 GCTTCTCTTTATTTAATCAGACACAATTCGATTTTAAATCAATTGTCTATTCAATCAATGACAAT
1 GCTTCTCTTTATTCAATCAGACACAACTCGATTTTAAATCAATTGTCTATTCAATCAATGACAAC
*
44120 TCAATTCTAAATTAAT
66 TCAATCCTAAATTAAT
44136 CGAGATTCTA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (85 bp):
GCTTCTCTTTATTCAATCAGACACAACTCGATTTTAAATCAATTGTCTATTCAATCAATGACAAC
TCAATCCTAAATTAATTAGA
Found at i:46401 original size:42 final size:43
Alignment explanation
Indices: 46342--46427 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
46332 AAACACATAA
* * *
46342 ATAAATAAACTGCTGAACCCACATT-CTGTGGGACTTGAACCC
1 ATAAACAAACTGCTGAACCCACATTCCCGTGGAACTTGAACCC
*
46384 ATAAACAAACTGTTGAACCCACATTCCCGTGGAACTTGAACCC
1 ATAAACAAACTGCTGAACCCACATTCCCGTGGAACTTGAACCC
46427 A
1 A
46428 GGACCTTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 23 0.59
43 16 0.41
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (43 bp):
ATAAACAAACTGCTGAACCCACATTCCCGTGGAACTTGAACCC
Found at i:61554 original size:79 final size:80
Alignment explanation
Indices: 61457--61615 Score: 277
Period size: 79 Copynumber: 2.0 Consensus size: 80
61447 ATTTTATTTT
*
61457 GAGTTAATGGTTTTGGTTTTATAACTCTGTAAAAAATTACTAAAACGAGG-CGATAAGGTCTCAT
1 GAGTTAATGGTTTTGGTTTTATAACTCTGTAAAAAATTACTAAAACG-GGCCGATAAGGTCTCAC
*
61521 CAGATTAAAAGTTGGA
65 CAGATCAAAAGTTGGA
61537 GAGTTAATGG-TTTGGTTTTATAACTCTGTAAAAAATTACTAAAACGGGCCGATAAGGTCTCACC
1 GAGTTAATGGTTTTGGTTTTATAACTCTGTAAAAAATTACTAAAACGGGCCGATAAGGTCTCACC
61601 AGATCAAAAGTTGGA
66 AGATCAAAAGTTGGA
61616 AGGACTGTTA
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
78 2 0.03
79 64 0.84
80 10 0.13
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (80 bp):
GAGTTAATGGTTTTGGTTTTATAACTCTGTAAAAAATTACTAAAACGGGCCGATAAGGTCTCACC
AGATCAAAAGTTGGA
Found at i:62262 original size:21 final size:24
Alignment explanation
Indices: 62222--62265 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 24
62212 TTAATCATTA
62222 AACTACTCCTCAATATTATCCACT
1 AACTACTCCTCAATATTATCCACT
62246 AACTAC-CCT-AA-ATTATCCAC
1 AACTACTCCTCAATATTATCCAC
62266 ACGTTATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 3 0.15
24 6 0.30
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.30
Consensus pattern (24 bp):
AACTACTCCTCAATATTATCCACT
Found at i:63547 original size:55 final size:55
Alignment explanation
Indices: 63480--63623 Score: 263
Period size: 55 Copynumber: 2.6 Consensus size: 55
63470 GATTTCGTTA
63480 ATTTTCCATATGATCACTTTTGTATATTTTATTTTTCTAATGTATGATCTGTTTT
1 ATTTTCCATATGATCACTTTTGTATATTTTATTTTTCTAATGTATGATCTGTTTT
63535 ATTTTCCATATGATCACTTTTGTATATTTTATTTTTCTAATGTATGATCTGTTTT
1 ATTTTCCATATGATCACTTTTGTATATTTTATTTTTCTAATGTATGATCTGTTTT
*
63590 ATTTTCCATATGATCACTTTCGT-TAATTTTATTT
1 ATTTTCCATATGATCACTTTTGTAT-ATTTTATTT
63624 CATGGAAATT
Statistics
Matches: 87, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
54 1 0.01
55 86 0.99
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (55 bp):
ATTTTCCATATGATCACTTTTGTATATTTTATTTTTCTAATGTATGATCTGTTTT
Found at i:63565 original size:30 final size:30
Alignment explanation
Indices: 63480--63569 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
63470 GATTTCGTTA
63480 ATTTTCCATATGATCACTTTTGTATATTTT
1 ATTTTCCATATGATCACTTTTGTATATTTT
* * *
63510 ATTTTTC-TAATG-T-A----TGATCTGTTTT
1 ATTTTCCAT-ATGATCACTTTTG-TATATTTT
63535 ATTTTCCATATGATCACTTTTGTATATTTT
1 ATTTTCCATATGATCACTTTTGTATATTTT
63565 ATTTT
1 ATTTT
63570 TCTAATGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
24 2 0.04
25 15 0.33
26 2 0.04
27 1 0.02
28 1 0.02
29 2 0.04
30 20 0.44
31 2 0.04
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59
Consensus pattern (30 bp):
ATTTTCCATATGATCACTTTTGTATATTTT
Found at i:63593 original size:30 final size:30
Alignment explanation
Indices: 63504--63594 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
63494 CACTTTTGTA
63504 TATTTTATTTTTCTAATGTATGATCTG---
1 TATTTTATTTTTCTAATGTATGATCTGTTT
* * *
63531 --TTTTA-TTTTCCATATG-ATCA-CTTTTGT
1 TATTTTATTTTTCTA-ATGTATGATCTGTT-T
63558 ATATTTTATTTTTCTAATGTATGATCTGTTT
1 -TATTTTATTTTTCTAATGTATGATCTGTTT
63589 TATTTT
1 TATTTT
63595 CCATATGATC
Statistics
Matches: 47, Mismatches: 6, Indels: 19
0.65 0.08 0.26
Matches are distributed among these distances:
23 2 0.04
24 9 0.19
25 8 0.17
30 14 0.30
31 10 0.21
32 4 0.09
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (30 bp):
TATTTTATTTTTCTAATGTATGATCTGTTT
Done.