Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011962.1 Corchorus olitorius cultivar O-4 contig11995, 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: 38863
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:586 original size:13 final size:14
Alignment explanation
Indices: 576--619 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
566 AACAATTTAT
576 TAAAACCAT-TT-A
1 TAAAACCATATTAA
588 TAAAA-CATATTAA
1 TAAAACCATATTAA
601 TAAAA-CATATTAA
1 TAAAACCATATTAA
614 TAAAAC
1 TAAAAC
620 AGTTCCTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.10
12 7 0.24
13 19 0.66
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAACCATATTAA
Found at i:592 original size:25 final size:27
Alignment explanation
Indices: 564--620 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
554 TCATGCACCC
*
564 AAAACAAT-TTATTAAAACCAT-TT-AT
1 AAAACAATATTAATAAAA-CATATTAAT
589 AAAAC-ATATTAATAAAACATATTAAT
1 AAAACAATATTAATAAAACATATTAAT
615 AAAACA
1 AAAACA
621 GTTCCTCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAACAATATTAATAAAACATATTAAT
Found at i:620 original size:13 final size:13
Alignment explanation
Indices: 587--620 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
577 AAAACCATTT
587 ATAAAACATATTA
1 ATAAAACATATTA
600 ATAAAACATATTA
1 ATAAAACATATTA
613 ATAAAACA
1 ATAAAACA
621 GTTCCTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAACATATTA
Found at i:1990 original size:3 final size:3
Alignment explanation
Indices: 1984--2017 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1974 TTTTTTTTTC
*
1984 CTT CTT CTT CTT CTT CTT CTT CTT CTT CCT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
2018 CCGGTCGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:3563 original size:22 final size:22
Alignment explanation
Indices: 3538--3581 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3528 TCCAAGGCTT
*
3538 CAAACACGCTTCAACAGCTACA
1 CAAACAAGCTTCAACAGCTACA
*
3560 CAAACAAGCTTCTACAGCTACA
1 CAAACAAGCTTCAACAGCTACA
3582 AACTTGCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.34, G:0.09, T:0.16
Consensus pattern (22 bp):
CAAACAAGCTTCAACAGCTACA
Found at i:6104 original size:11 final size:11
Alignment explanation
Indices: 6090--6122 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6080 TTCTTTCTCC
6090 TGTTTTGGTTT
1 TGTTTTGGTTT
6101 TGTTTTGG-TT
1 TGTTTTGGTTT
*
6111 TGTTTTTGTTT
1 TGTTTTGGTTT
6122 T
1 T
6123 TGTCTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (11 bp):
TGTTTTGGTTT
Found at i:6831 original size:77 final size:77
Alignment explanation
Indices: 6724--6877 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 77
6714 GACAGGGGAG
*
6724 AAATTGTCCCGATTTTGATAGTTTAGGGGTAAAAGTTCCAAAAAAATTCTAAACTTTTTTTGTTC
1 AAATTGTCCCGATTTTGATAATTTAGGGGTAAAAGTTCCAAAAAAATTC-AAACTTTTTTTGTTC
6789 AAAGGGTAAAAGT
65 AAAGGGTAAAAGT
* *
6802 AAATTGTCCCGA-TTTGATAATTTAGGGGTAAAAGTTCCAAAAAAATTCCAATTTTTTTTGTTCA
1 AAATTGTCCCGATTTTGATAATTTAGGGGTAAAAGTTCCAAAAAAATTCAAACTTTTTTTGTTCA
6866 AAGGGTAAAAGT
66 AAGGGTAAAAGT
6878 TCCAAATTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
76 26 0.36
77 35 0.48
78 12 0.16
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (77 bp):
AAATTGTCCCGATTTTGATAATTTAGGGGTAAAAGTTCCAAAAAAATTCAAACTTTTTTTGTTCA
AAGGGTAAAAGT
Found at i:9031 original size:29 final size:29
Alignment explanation
Indices: 8990--9061 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
8980 GATCAATTTG
*
8990 GGGGCCAAACGTTTCAATTGTAACAAAAT
1 GGGGCCAAACGTTTCAATTGAAACAAAAT
*
9019 GGGGCCAAACGTTTCAATTGAAATAAAAT
1 GGGGCCAAACGTTTCAATTGAAACAAAAT
*
9048 GGGGCCAAAAGTTT
1 GGGGCCAAACGTTT
9062 TCGGGACTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (29 bp):
GGGGCCAAACGTTTCAATTGAAACAAAAT
Found at i:9877 original size:60 final size:60
Alignment explanation
Indices: 9759--9934 Score: 255
Period size: 60 Copynumber: 3.0 Consensus size: 60
9749 GATGGTATGC
* ** * * *
9759 ATTCGAATAAAATATACAGTAAG-TTGGAATTTTTTTTTGTTTTATGTGTTGGGCTTTGT
1 ATTCGAATATAATATATGGGAAGTTTGTAATTTTTTTTTGTTTTATGTGTTGGGTTTTGT
9818 ATTCGAATATAATATATGGGAAGTTTGTAATTTTTTTTTGTTTTATGTGTTGGGTTTTGT
1 ATTCGAATATAATATATGGGAAGTTTGTAATTTTTTTTTGTTTTATGTGTTGGGTTTTGT
* * * *
9878 ATTTGAATATAATATATGGGAAGTTGGTAAATTTTCTTTGTTTTATGTGTTGGGTTT
1 ATTCGAATATAATATATGGGAAGTTTGTAATTTTTTTTTGTTTTATGTGTTGGGTTT
9935 CTGACTTGGT
Statistics
Matches: 106, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
59 19 0.18
60 87 0.82
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.52
Consensus pattern (60 bp):
ATTCGAATATAATATATGGGAAGTTTGTAATTTTTTTTTGTTTTATGTGTTGGGTTTTGT
Found at i:9955 original size:44 final size:44
Alignment explanation
Indices: 9905--9998 Score: 188
Period size: 44 Copynumber: 2.1 Consensus size: 44
9895 GGGAAGTTGG
9905 TAAATTTTCTTTGTTTTATGTGTTGGGTTTCTGACTTGGTGAGA
1 TAAATTTTCTTTGTTTTATGTGTTGGGTTTCTGACTTGGTGAGA
9949 TAAATTTTCTTTGTTTTATGTGTTGGGTTTCTGACTTGGTGAGA
1 TAAATTTTCTTTGTTTTATGTGTTGGGTTTCTGACTTGGTGAGA
9993 TAAATT
1 TAAATT
9999 GAATATTTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.18, C:0.06, G:0.23, T:0.52
Consensus pattern (44 bp):
TAAATTTTCTTTGTTTTATGTGTTGGGTTTCTGACTTGGTGAGA
Found at i:10116 original size:17 final size:17
Alignment explanation
Indices: 10094--10126 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10084 AGATGTTTTC
10094 TGTATGCTTTGGATTTG
1 TGTATGCTTTGGATTTG
*
10111 TGTATGCTTTGTATTT
1 TGTATGCTTTGGATTT
10127 AAATAATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.58
Consensus pattern (17 bp):
TGTATGCTTTGGATTTG
Found at i:10635 original size:9 final size:9
Alignment explanation
Indices: 10623--10664 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
10613 GAATGTAAAT
10623 AATGGTGAC
1 AATGGTGAC
10632 AATGGTGAC
1 AATGGTGAC
* *
10641 AAT-GTAAAT
1 AATGGT-GAC
10650 AATGGTGAC
1 AATGGTGAC
10659 AATGGT
1 AATGGT
10665 CAGGATGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.38, C:0.07, G:0.29, T:0.26
Consensus pattern (9 bp):
AATGGTGAC
Found at i:10635 original size:27 final size:27
Alignment explanation
Indices: 10605--10673 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
10595 AGATGGTCAG
10605 AATGGTGAGAATGTAAATAATGGTGAC
1 AATGGTGAGAATGTAAATAATGGTGAC
*
10632 AATGGTGACAATGTAAATAATGGTGAC
1 AATGGTGAGAATGTAAATAATGGTGAC
* *
10659 AATGGTCAGGATGTA
1 AATGGTGAGAATGTA
10674 GATGGTGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (27 bp):
AATGGTGAGAATGTAAATAATGGTGAC
Found at i:10779 original size:21 final size:21
Alignment explanation
Indices: 10755--10808 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
10745 TGAAAAAGAT
10755 GAAGAGAGGGTT-CAGGTAAAG
1 GAAGAGAGGGTTCCA-GTAAAG
* *
10776 GAAGAGAGGGTTCCAGTAGAT
1 GAAGAGAGGGTTCCAGTAAAG
10797 GAAGAGAGGGTT
1 GAAGAGAGGGTT
10809 GATCAGGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.35, C:0.06, G:0.43, T:0.17
Consensus pattern (21 bp):
GAAGAGAGGGTTCCAGTAAAG
Found at i:10830 original size:6 final size:6
Alignment explanation
Indices: 10819--10854 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
10809 GATCAGGGTC
* *
10819 AGTCTG ATTCTG AGTCTG AGTCTG AGTCTG ATTCTG
1 AGTCTG AGTCTG AGTCTG AGTCTG AGTCTG AGTCTG
10855 GCAGTGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (6 bp):
AGTCTG
Found at i:10836 original size:12 final size:12
Alignment explanation
Indices: 10819--10854 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
10809 GATCAGGGTC
10819 AGTCTGATTCTG
1 AGTCTGATTCTG
*
10831 AGTCTGAGTCTG
1 AGTCTGATTCTG
10843 AGTCTGATTCTG
1 AGTCTGATTCTG
10855 GCAGTGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (12 bp):
AGTCTGATTCTG
Found at i:22122 original size:11 final size:11
Alignment explanation
Indices: 22108--22149 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
22098 ATTCATAACA
22108 AATTTATAATT
1 AATTTATAATT
22119 AATTTATAATT
1 AATTTATAATT
22130 -ATTTGATAATGT
1 AATTT-ATAAT-T
*
22142 ATTTTATA
1 AATTTATA
22150 TAGGAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 16 0.59
12 4 0.15
13 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:23151 original size:7 final size:7
Alignment explanation
Indices: 23137--23344 Score: 409
Period size: 7 Copynumber: 29.9 Consensus size: 7
23127 TTTTGAGCCA
23137 TGAA-TT
1 TGAATTT
23143 TGAATTT
1 TGAATTT
23150 TGAATTT
1 TGAATTT
23157 TGAATTT
1 TGAATTT
23164 TGAATTT
1 TGAATTT
23171 TGAATTT
1 TGAATTT
23178 TGAATTT
1 TGAATTT
23185 TGAATTT
1 TGAATTT
23192 TGAATTT
1 TGAATTT
23199 TGAATTT
1 TGAATTT
23206 TGAATTT
1 TGAATTT
23213 TGAATTT
1 TGAATTT
23220 TGAATTT
1 TGAATTT
23227 TGAATTT
1 TGAATTT
23234 TGAATTT
1 TGAATTT
23241 TGAATTT
1 TGAATTT
23248 TGAATTT
1 TGAATTT
23255 TGAATTT
1 TGAATTT
23262 TGAATTT
1 TGAATTT
23269 TGAATTT
1 TGAATTT
23276 TGAATTT
1 TGAATTT
23283 TGAATTT
1 TGAATTT
23290 TGAATTT
1 TGAATTT
23297 TGAATTT
1 TGAATTT
23304 TGAATTT
1 TGAATTT
23311 TGAATTT
1 TGAATTT
23318 TGAATTT
1 TGAATTT
23325 TGAATTT
1 TGAATTT
23332 TGAATTT
1 TGAATTT
23339 TGAATT
1 TGAATT
23345 GCCTATTTGG
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
6 4 0.02
7 197 0.98
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (7 bp):
TGAATTT
Found at i:23540 original size:33 final size:33
Alignment explanation
Indices: 23498--23575 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
23488 AGAAACTGTG
* * *
23498 GATTTTGAACTTTGAGTTTTGATATGATATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
23531 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
1 GATTTTGAACTTTGAATTTTGAAATGAAATGCA
*
23564 AATTTTGAACTT
1 GATTTTGAACTT
23576 CTTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (33 bp):
GATTTTGAACTTTGAATTTTGAAATGAAATGCA
Found at i:23768 original size:54 final size:54
Alignment explanation
Indices: 23703--23981 Score: 398
Period size: 54 Copynumber: 5.2 Consensus size: 54
23693 GACCACGCTG
* * * * * *
23703 GATCAACTTAGATTTTTGAAAACTTCTATGGAAGACCACACAGAGTCATCTGAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
* *
23757 TATCAACTTAGACCTCT-AAAAGCTTCTATGAAAGACCACACTGGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAA-CTTCTATGAAAGACCACACTGGGTCATCTTAA
* * *
23811 GATCAACTTAGATCTCTGAAAACTTTTATGAAAGACCACACTTGGTCATCCTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
*
23865 GATCAACTTAGATCTCTAAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
* * * *
23919 GATCAACTTAGATCCCTGAAAACTTCTATGAAAGACCACACTGGATAAACTTAA
1 GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
23973 GATCAACTT
1 GATCAACTT
23982 TCTAGAGAGA
Statistics
Matches: 201, Mismatches: 22, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
53 4 0.02
54 193 0.96
55 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (54 bp):
GATCAACTTAGATCTCTGAAAACTTCTATGAAAGACCACACTGGGTCATCTTAA
Found at i:24134 original size:37 final size:37
Alignment explanation
Indices: 24088--24321 Score: 296
Period size: 37 Copynumber: 6.4 Consensus size: 37
24078 GATTTTGAAG
* *
24088 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * * *
24125 AGAAACCTAAACAGGGATCTTGAACAA-GATTTTGATG
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGATA
24162 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
24199 AGACACCTAAACA-GGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* * * *
24235 AGACACCTAAACAGGAATCTTGAACAA-GATTTTGATGA
1 AGACACCTAAACAGGGACCTTAAATAAGGA-TTTGAT-A
* *
24273 A-ATACCTAAATAGGGACCTTAAATAAGGATTTGATA
1 AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
24309 AGACACCTAAACA
1 AGACACCTAAACA
24322 AAAATCTTGA
Statistics
Matches: 166, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
36 42 0.25
37 118 0.71
38 6 0.04
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (37 bp):
AGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
Found at i:24243 original size:110 final size:111
Alignment explanation
Indices: 24088--24321 Score: 407
Period size: 110 Copynumber: 2.1 Consensus size: 111
24078 GATTTTGAAG
*
24088 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGGATCTTGAACAAG
1 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
*
24153 ATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATA
66 ATTTTGATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATA
* *
24199 AGACACCTAAACAGG-ACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAG
1 AGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
* *
24263 ATTTTGATGAAATACCTAAATAGGGACCTTAAATAAGGATTTGATA
66 ATTTTGATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATA
24309 AGACACCTAAACA
1 AGACACCTAAACA
24322 AAAATCTTGA
Statistics
Matches: 117, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 102 0.87
111 15 0.13
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (111 bp):
AGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAG
ATTTTGATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATA
Found at i:24328 original size:74 final size:73
Alignment explanation
Indices: 24203--24346 Score: 243
Period size: 74 Copynumber: 2.0 Consensus size: 73
24193 TTGATAAGAC
**
24203 ACCTAAACAGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGATTTT
1 ACCTAAACAGGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCTTGAACAAGATTTT
24268 GATGAAAT
66 GATGAAAT
* *
24276 ACCTAAATAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCTTGAACAAGGTTT
1 ACCTAAACA-GGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCTTGAACAAGATTT
24341 TGATGA
65 TGATGA
24347 GACTGAATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 8 0.12
74 58 0.88
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (73 bp):
ACCTAAACAGGACCTTAAATAAGGATTTGATAAGACACCTAAACAAAAATCTTGAACAAGATTTT
GATGAAAT
Found at i:25327 original size:19 final size:20
Alignment explanation
Indices: 25303--25345 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
25293 AACCTTTTGA
* *
25303 TTTTTCTTT-CTTTTTTCTT
1 TTTTTCTTTGCTTTCTCCTT
25322 TTTTTCTTTGCTTTCTCCTT
1 TTTTTCTTTGCTTTCTCCTT
25342 TTTT
1 TTTT
25346 GCTGCACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTGCTTTCTCCTT
Found at i:26008 original size:14 final size:14
Alignment explanation
Indices: 25978--26015 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
25968 ACTCAAAACC
25978 TTTTTGAAAACTCA
1 TTTTTGAAAACTCA
25992 TTTCTTGAAAA-TCA
1 TTT-TTGAAAACTCA
26006 TTTTTGAAAA
1 TTTTTGAAAA
26016 ACGTCCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.30
14 9 0.39
15 7 0.30
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACTCA
Found at i:31938 original size:3 final size:3
Alignment explanation
Indices: 31930--31992 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
31920 CGTAAGGATT
31930 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
31978 TTA TTA GTA TT- TTA T
1 TTA TTA TTA TTA TTA T
31993 GAAGTTCAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34248 original size:16 final size:17
Alignment explanation
Indices: 34218--34250 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34208 ATTTTACTTT
*
34218 AAAAAATATATATTTAA
1 AAAAAATATAAATTTAA
34235 AAAAAATA-AAATTTAA
1 AAAAAATATAAATTTAA
34251 GTGGGTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAATATAAATTTAA
Found at i:35690 original size:59 final size:63
Alignment explanation
Indices: 35606--35749 Score: 206
Period size: 67 Copynumber: 2.3 Consensus size: 63
35596 AAATTTAATC
* *
35606 GACACCAGAAGTTGTCATAT-TAA-ATTATCTTGACGCCAGAAGTTGTCA-TGA-AAATTATT
1 GACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATTATT
35665 GACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGAAATTA
1 GACACCAGAAGTTGTCATATCAAA-TATTATCTTGACACCAGAAGTTGTCA--CTGA-GAAATTA
35730 TT
62 TT
35732 GACACCAGAAGTTGTCAT
1 GACACCAGAAGTTGTCAT
35750 CCCAAGATTG
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
59 20 0.27
60 2 0.03
62 24 0.32
65 3 0.04
67 26 0.35
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (63 bp):
GACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATTATT
Found at i:35701 original size:34 final size:31
Alignment explanation
Indices: 35606--35749 Score: 154
Period size: 33 Copynumber: 4.6 Consensus size: 31
35596 AAATTTAATC
*
35606 GACACCAGAAGTTGTCATATTAAATTATCTT
1 GACACCAGAAGTTGTCATATAAAATTATCTT
* *
35637 GACGCCAGAAGTTGTCAT-GAAAATTA--TT
1 GACACCAGAAGTTGTCATATAAAATTATCTT
35665 GACACCAGAAGTTGTCATATCAAATTATTATCTT
1 GACACCAGAAGTTGTCATAT-AAA--ATTATCTT
*
35699 GACACCAGAAGTTGTCATGCTGAGGAAATTA--TT
1 GACACCAGAAGTTGTCAT-AT-A--AAATTATCTT
35732 GACACCAGAAGTTGTCAT
1 GACACCAGAAGTTGTCAT
35750 CCCAAGATTG
Statistics
Matches: 97, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
28 19 0.20
30 9 0.09
31 17 0.18
32 4 0.04
33 20 0.21
34 20 0.21
35 6 0.06
37 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (31 bp):
GACACCAGAAGTTGTCATATAAAATTATCTT
Done.