Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012495.1 Corchorus olitorius cultivar O-4 contig12528, 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: 65414
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:229 original size:33 final size:33
Alignment explanation
Indices: 155--217 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
145 GTGGTGATGG
155 CAACCATGGCATGCCGCCCTACTAGGGTGGCAC
1 CAACCATGGCATGCCGCCCTACTAGGGTGGCAC
*
188 CAACCATGGCATGCCGCCCTCCTAGGGTGG
1 CAACCATGGCATGCCGCCCTACTAGGGTGG
218 TAGTGACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.19, C:0.37, G:0.29, T:0.16
Consensus pattern (33 bp):
CAACCATGGCATGCCGCCCTACTAGGGTGGCAC
Found at i:908 original size:16 final size:16
Alignment explanation
Indices: 887--941 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
877 TTGAGGATTT
887 GTTGAAGAAATTGAAG
1 GTTGAAGAAATTGAAG
*
903 GTTGAAGAAGTTTGAA-
1 GTTGAAGAA-ATTGAAG
* *
919 GTTGTTAGAAAATGAAG
1 GTTG-AAGAAATTGAAG
936 GTTGAA
1 GTTGAA
942 AAAGTTTGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (16 bp):
GTTGAAGAAATTGAAG
Found at i:935 original size:33 final size:34
Alignment explanation
Indices: 892--955 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
882 GATTTGTTGA
* *
892 AGAAATTGAAGGTTGAAGAAGTTTGA-AGTTGTT
1 AGAAAATGAAGGTTGAAAAAGTTTGAGAGTTGTT
925 AGAAAATGAAGGTTGAAAAAGTTTGAGAGTT
1 AGAAAATGAAGGTTGAAAAAGTTTGAGAGTT
956 TTAAGAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (34 bp):
AGAAAATGAAGGTTGAAAAAGTTTGAGAGTTGTT
Found at i:1164 original size:44 final size:42
Alignment explanation
Indices: 1095--1185 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 42
1085 TTATTTATTC
1095 ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATAA
1 ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATAA
1137 ATTATGTAAAAAAAAACAAATTACTAATTATAAATTTATCATAA
1 ATTATGT--AAAAAAACAAATTACTAATTATAAATTTATCATAA
1181 ATTAT
1 ATTAT
1186 TTCTAGAACT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 7 0.15
44 40 0.85
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (42 bp):
ATTATGTAAAAAAACAAATTACTAATTATAAATTTATCATAA
Found at i:1599 original size:18 final size:18
Alignment explanation
Indices: 1550--1593 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1540 AAACTCAGGA
1550 GTCGTTTGACATTGTTTT
1 GTCGTTTGACATTGTTTT
1568 GTCGTTTGACATTGTTTT
1 GTCGTTTGACATTGTTTT
1586 -T-GTTTGAC
1 GTCGTTTGAC
1594 TAATTGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 18 0.69
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (18 bp):
GTCGTTTGACATTGTTTT
Found at i:1674 original size:60 final size:60
Alignment explanation
Indices: 1601--1765 Score: 195
Period size: 61 Copynumber: 2.7 Consensus size: 60
1591 GACTAATTGC
* *
1601 TCAAATAAAGGCCTAACGTTTGCCAAAATGCTCAAATAAAGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAAGGCCCGATCTTTTAATTTGG
* * * * *** *
1661 TCAAATAAGGGCCTAACATTTACCAAAATAATCAAAATAAGGGTTTGGTCTTTTAATTTGG
1 TCAAATAAGGGCCTAACGTTTGCCAAAATACTC-AAATAAAGGCCCGATCTTTTAATTTGG
* * * *
1722 CCAAATAAGCGTCTAACGTTTGCCAAAATTCTCAAATAAAGGCC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAAGGCC
1766 TGGCATCGAA
Statistics
Matches: 84, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 36 0.43
61 48 0.57
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (60 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAAGGCCCGATCTTTTAATTTGG
Found at i:1839 original size:59 final size:63
Alignment explanation
Indices: 1772--1898 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 63
1762 GGCCTGGCAT
1772 CGAAAATTTTCACGTG-T-C-A-TCCAAACTAATGTCAAGCCCTTATTGAGCATTTTGGCAAA
1 CGAAAATTTTCACGTGATCCAATTCCAAACTAATGTCAAGCCCTTATTGAGCATTTTGGCAAA
1831 CGAAAATTTTCACGTGTCATCCAAATTCCAAACTAATGTCAAGCCCTTATTGAGCATTTTGGCAA
1 CGAAAATTTTCACGTG--ATCC-AATTCCAAACTAATGTCAAGCCCTTATTGAGCATTTTGGCAA
1896 A
63 A
1897 CG
1 CG
1899 TTAGGCCCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
59 16 0.26
62 1 0.02
63 1 0.02
65 1 0.02
66 42 0.69
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (63 bp):
CGAAAATTTTCACGTGATCCAATTCCAAACTAATGTCAAGCCCTTATTGAGCATTTTGGCAAA
Found at i:1943 original size:23 final size:23
Alignment explanation
Indices: 1913--1966 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1903 GCCCTTATTT
* *
1913 TTATTTGATAAAAGATCAAGCCC
1 TTATTTGATAAAAAATCAAGCAC
**
1936 TTATTTGATAAAAAATCGGGCAC
1 TTATTTGATAAAAAATCAAGCAC
1959 TTATTTGA
1 TTATTTGA
1967 GCATTTTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (23 bp):
TTATTTGATAAAAAATCAAGCAC
Found at i:2133 original size:34 final size:34
Alignment explanation
Indices: 2089--2153 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2079 GTTAGAAGTA
* *
2089 TTTTGGAAAAACATGTAAACACAAAATTCTTGTG
1 TTTTGAAAAAACATGAAAACACAAAATTCTTGTG
2123 TTTTGAAAAAACATGAAAACACAAAATTCTT
1 TTTTGAAAAAACATGAAAACACAAAATTCTT
2154 AATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (34 bp):
TTTTGAAAAAACATGAAAACACAAAATTCTTGTG
Found at i:2222 original size:36 final size:36
Alignment explanation
Indices: 2180--2296 Score: 135
Period size: 36 Copynumber: 3.0 Consensus size: 36
2170 AAAATGTTTC
2180 TGTTTCCAAAATTTTTGAAAACATAAACACAGAAAA
1 TGTTTCCAAAATTTTTGAAAACATAAACACAGAAAA
2216 TGTTTCCAAAATTTTTGAAAACATAAACATAGACGTAGAAAA
1 TGTTTCCAAAATTTTTGAAAACATAAAC----AC--AGAAAA
* *
2258 CGATTTCCAAAATTTTTTGAAAACATAAAACAAAGAAAA
1 TG-TTTCCAAAA-TTTTTGAAAACAT-AAACACAGAAAA
2297 CGGAAATTCC
Statistics
Matches: 70, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
36 28 0.40
39 6 0.09
40 2 0.03
41 1 0.01
42 7 0.10
43 9 0.13
44 13 0.19
45 4 0.06
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.27
Consensus pattern (36 bp):
TGTTTCCAAAATTTTTGAAAACATAAACACAGAAAA
Found at i:2400 original size:75 final size:75
Alignment explanation
Indices: 2317--2458 Score: 275
Period size: 75 Copynumber: 1.9 Consensus size: 75
2307 AAACGAGCTC
*
2317 TATTTTAATTTTCACTAGTGCTCAATTTTTATATTTCAATTATTAATTTTCCTTTAAAGTACAAG
1 TATTTTAATTTTCACAAGTGCTCAATTTTTATATTTCAATTATTAATTTTCCTTTAAAGTACAAG
2382 TAAAACGCCT
66 TAAAACGCCT
2392 TATTTTAATTTTCACAAGTGCTCAATTTTTATATTTCAATTATTAATTTTCCTTTAAAGTACAAG
1 TATTTTAATTTTCACAAGTGCTCAATTTTTATATTTCAATTATTAATTTTCCTTTAAAGTACAAG
2457 TA
66 TA
2459 CAACTTTACA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (75 bp):
TATTTTAATTTTCACAAGTGCTCAATTTTTATATTTCAATTATTAATTTTCCTTTAAAGTACAAG
TAAAACGCCT
Found at i:11669 original size:17 final size:17
Alignment explanation
Indices: 11647--11681 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11637 ATAGTGAATA
*
11647 TAAAATTTCATCTATAT
1 TAAAATTTCATCCATAT
11664 TAAAATTTCATCCATAT
1 TAAAATTTCATCCATAT
11681 T
1 T
11682 GTATACTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTTCATCCATAT
Found at i:13292 original size:11 final size:11
Alignment explanation
Indices: 13276--13307 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
13266 GCTCGATTAA
13276 TGTTCGTTTAG
1 TGTTCGTTTAG
*
13287 TGTTCGTTTAT
1 TGTTCGTTTAG
13298 TGTTCGTTTA
1 TGTTCGTTTA
13308 ATAGATCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (11 bp):
TGTTCGTTTAG
Found at i:13586 original size:20 final size:20
Alignment explanation
Indices: 13563--13631 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
13553 TATATATATA
13563 ATAATTATAATTTTATTTAT
1 ATAATTATAATTTTATTTAT
* ** *
13583 ATAAATATTAA-AATATGTAT
1 ATAATTA-TAATTTTATTTAT
*
13603 ATAATTAT-ATTTTATTCCAT
1 ATAATTATAATTTTATT-TAT
13623 ATAA-TATAA
1 ATAATTATAA
13632 ATAATATATA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
18 1 0.03
19 7 0.19
20 25 0.69
21 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (20 bp):
ATAATTATAATTTTATTTAT
Found at i:13610 original size:40 final size:40
Alignment explanation
Indices: 13554--13644 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 40
13544 TAATTACCCT
* *
13554 ATATATATAATAATTATAATTTTATT-TATATAAATATTAA-A
1 ATATATAT-ATAATTAT-ATTTTATTCCATAT-AATATAAATA
*
13595 ATATGTATATAATTATATTTTATTCCATATAATATAAATA
1 ATATATATATAATTATATTTTATTCCATATAATATAAATA
13635 ATATATATAT
1 ATATATATAT
13645 TTATTCCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
39 15 0.34
40 22 0.50
41 7 0.16
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (40 bp):
ATATATATATAATTATATTTTATTCCATATAATATAAATA
Found at i:17708 original size:28 final size:32
Alignment explanation
Indices: 17657--17739 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 32
17647 AATTAGCAAA
* *
17657 AAATATTTATATACATTTACTA-T-T-TGGAAT
1 AAATATATATAT-TATTTACTATTATATGGAAT
17687 AAATATATATATTATTTA-TATTATATGGAAT
1 AAATATATATATTATTTACTATTATATGGAAT
*
17718 AAA-ATATA-ATTATATACATATT
1 AAATATATATATTATTTAC-TATT
17740 TTAATATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.04
29 13 0.29
30 17 0.38
31 13 0.29
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (32 bp):
AAATATATATATTATTTACTATTATATGGAAT
Found at i:17739 original size:31 final size:33
Alignment explanation
Indices: 17654--17739 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 33
17644 TGTAATTAGC
* *
17654 AAAAAATATTTATATACAT-TTACTATTTGGAAT
1 AAAATATAATTATATACATATTACTA-TTGGAAT
*
17687 AAATATATATATTAT-T-TATATTA-TA-TGGAAT
1 AAA-ATATA-ATTATATACATATTACTATTGGAAT
17718 AAAATATAATTATATACATATT
1 AAAATATAATTATATACATATT
17740 TTAATATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
29 5 0.11
30 6 0.14
31 14 0.32
33 7 0.16
34 8 0.18
35 4 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (33 bp):
AAAATATAATTATATACATATTACTATTGGAAT
Found at i:17739 original size:40 final size:40
Alignment explanation
Indices: 17689--17779 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 40
17679 TTTGGAATAA
* *
17689 ATATATATATTATTTATA-TTATATGGAAT-AAAATATAATT
1 ATATATATATT-TTAATATTTATAT-AAATAAAAATATAATT
*
17729 ATATACATATTTTAATATTTATATAAATAAAAATATAATT
1 ATATATATATTTTAATATTTATATAAATAAAAATATAATT
17769 ATTATATATAT
1 A-TATATATAT
17780 AATATAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
39 8 0.18
40 28 0.64
41 8 0.18
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (40 bp):
ATATATATATTTTAATATTTATATAAATAAAAATATAATT
Found at i:17833 original size:11 final size:11
Alignment explanation
Indices: 17817--17848 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
17807 AACGATCTAT
17817 TAAACGAACAA
1 TAAACGAACAA
*
17828 TAAACGAACAC
1 TAAACGAACAA
17839 TAAACGAACA
1 TAAACGAACA
17849 TTAATCGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.09
Consensus pattern (11 bp):
TAAACGAACAA
Found at i:21086 original size:3 final size:3
Alignment explanation
Indices: 21078--21102 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21068 TAAGAAACAC
21078 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
21103 ATTACTAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:32549 original size:2 final size:2
Alignment explanation
Indices: 32542--32566 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32532 GAAATTACAC
32542 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
32567 ACTAACCGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35290 original size:19 final size:19
Alignment explanation
Indices: 35259--35306 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
35249 CTATTAGGGT
35259 TTAATTAATTAATGTTATT-A
1 TTAATT-ATTAATG-TATTCA
*
35279 TTATTTATTAATGTATTCA
1 TTAATTATTAATGTATTCA
35298 TTAATTATT
1 TTAATTATT
35307 TCCGCAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 16 0.64
20 5 0.20
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TTAATTATTAATGTATTCA
Found at i:37789 original size:18 final size:18
Alignment explanation
Indices: 37766--37801 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
37756 CATAGAAAAC
37766 ATAATAAGT-AAAGGAAAT
1 ATAATAAGTCAAA-GAAAT
37784 ATAATAAGTCAAAGAAAT
1 ATAATAAGTCAAAGAAAT
37802 TATTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.22
Consensus pattern (18 bp):
ATAATAAGTCAAAGAAAT
Found at i:39702 original size:28 final size:28
Alignment explanation
Indices: 39652--39707 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
39642 AATTAGTTCT
*
39652 AATTAAAATTAAGAATTTCTAAAAAAAA
1 AATTAAAATTAACAATTTCTAAAAAAAA
*
39680 AATTAAAATTTACATATTT-TAAAAAAAA
1 AATTAAAATTAACA-ATTTCTAAAAAAAA
39708 TATATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (28 bp):
AATTAAAATTAACAATTTCTAAAAAAAA
Found at i:39819 original size:13 final size:13
Alignment explanation
Indices: 39801--39825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39791 AACCCTTTTT
39801 CCCCTAATCTAAC
1 CCCCTAATCTAAC
39814 CCCCTAATCTAA
1 CCCCTAATCTAA
39826 TTCAACCTAG
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:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (13 bp):
CCCCTAATCTAAC
Found at i:42969 original size:11 final size:11
Alignment explanation
Indices: 42953--42978 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42943 CTTTGCCTAA
42953 AAAACTAGAAG
1 AAAACTAGAAG
42964 AAAACTAGAAG
1 AAAACTAGAAG
42975 AAAA
1 AAAA
42979 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:44883 original size:16 final size:16
Alignment explanation
Indices: 44862--44894 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
44852 GAAAAAATTA
44862 TGGCATATATTAAGAT
1 TGGCATATATTAAGAT
44878 TGGCATATATTAAGAT
1 TGGCATATATTAAGAT
44894 T
1 T
44895 ATGATGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TGGCATATATTAAGAT
Found at i:54330 original size:1 final size:1
Alignment explanation
Indices: 54326--54354 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
54316 TTTTTTGAAG
54326 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
54355 AGTTTAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:56126 original size:31 final size:31
Alignment explanation
Indices: 56088--56196 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
56078 TAAATTACCA
*
56088 ATTGACCCCACTAAAATTGAAGTTTTATCAT
1 ATTGACCCCACTAAAATTGAAGTTTTATCAC
* *
56119 ATTGACCCCAATAAAATTGAAATTTTATCAC
1 ATTGACCCCACTAAAATTGAAGTTTTATCAC
* *
56150 ATTGATCCTC-CTAAAA-TGAAAGATTTAT-AGC
1 ATTGA-CCCCACTAAAATTG-AAGTTTTATCA-C
*
56181 ATTGACCCCATTAAAA
1 ATTGACCCCACTAAAA
56197 ATGTTGGATA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
30 6 0.09
31 56 0.86
32 3 0.05
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (31 bp):
ATTGACCCCACTAAAATTGAAGTTTTATCAC
Found at i:57244 original size:49 final size:47
Alignment explanation
Indices: 57140--57280 Score: 169
Period size: 49 Copynumber: 3.0 Consensus size: 47
57130 GAGCGTGCCA
* * *
57140 ATCAATTTTGTC-AAAAATTGATAAAAAGTGCGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
57186 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
57235 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
57281 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
46 12 0.15
48 28 0.34
49 42 0.51
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Found at i:57676 original size:12 final size:13
Alignment explanation
Indices: 57650--57674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57640 TTTACTCTGA
57650 GGAGAGGTTTTTT
1 GGAGAGGTTTTTT
57663 GGAGAGGTTTTT
1 GGAGAGGTTTTT
57675 GGGGAGTATT
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:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (13 bp):
GGAGAGGTTTTTT
Found at i:58578 original size:9 final size:9
Alignment explanation
Indices: 58560--58599 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
58550 TTAATTCATT
58560 TAATTT-CA
1 TAATTTCCA
58568 TAATTTCCA
1 TAATTTCCA
*
58577 TAATTTCCT
1 TAATTTCCA
58586 TAATTTCC-
1 TAATTTCCA
58594 TAATTT
1 TAATTT
58600 GGGAGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 12 0.40
9 18 0.60
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTTCCA
Found at i:58580 original size:17 final size:17
Alignment explanation
Indices: 58560--58599 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
58550 TTAATTCATT
58560 TAATTT-CATAATTTCC
1 TAATTTCCATAATTTCC
*
58576 ATAATTTCCTTAATTTCC
1 -TAATTTCCATAATTTCC
58594 TAATTT
1 TAATTT
58600 GGGAGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTCCATAATTTCC
Done.