Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019835.1 Corchorus olitorius cultivar O-4 contig19868, 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: 114216
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3351 original size:75 final size:75
Alignment explanation
Indices: 3193--3490 Score: 395
Period size: 75 Copynumber: 4.0 Consensus size: 75
3183 ATTCAACGTA
* * * * * *
3193 AAGATTCCATATTCCGTAAGGATCGTAGCCATAAGTGCC-TTCCTTGTTGATGCTTTTGGCTTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTTATGCTTCTGGCCTAT
3257 GTAGCCCATC
66 GTAGCCCATC
* * * * *
3267 AAGATTCCATACTTAGCAAGGATCGTAGCCATAAGTGCCTTTCATTTTTTATACTTCTGGCTTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTTATGCTTCTGGCCTAT
*
3332 GTAGCCAATC
66 GTAGCCCATC
* *
3342 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTTCTTGTCTATGCTTCTGGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTTATGCTTCTGGCCTAT
3407 GTAGCCCATC
66 GTAGCCCATC
* * * *
3417 AA-ATTTCCATACTCAACAAGGATTGTAGCCATAAGTGCCCTTCCTTGTTAAT-CATTCTGGCCT
1 AAGA-TTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTTATGC-TTCTGGCCT
3480 ATGTAGCCCAT
64 ATGTAGCCCAT
3491 TAAAAAAGAA
Statistics
Matches: 197, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
74 37 0.19
75 160 0.81
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (75 bp):
AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTTATGCTTCTGGCCTAT
GTAGCCCATC
Found at i:3646 original size:37 final size:37
Alignment explanation
Indices: 3597--3764 Score: 219
Period size: 37 Copynumber: 4.5 Consensus size: 37
3587 GCTTACAGCC
3597 TATGCAGCTTAAAAGAGGGCTTACAACGCCTACAGTT
1 TATGCAGCTTAAAAGAGGGCTTACAACGCCTACAGTT
**
3634 TATGCAAATTAAAAGAGGGCTTACAACGCCTACAGTT
1 TATGCAGCTTAAAAGAGGGCTTACAACGCCTACAGTT
* * * **
3671 TATGCAGCTTAAAAGAGGGCATACAACACCTATAGCC
1 TATGCAGCTTAAAAGAGGGCTTACAACGCCTACAGTT
* * **
3708 TATGCAGCTTAAAATAGGGCTTACAACTCCTACAGCC
1 TATGCAGCTTAAAAGAGGGCTTACAACGCCTACAGTT
* *
3745 TATGCAGTTTAAAAAAGGGC
1 TATGCAGCTTAAAAGAGGGC
3765 ATTCTACGCA
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 116 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (37 bp):
TATGCAGCTTAAAAGAGGGCTTACAACGCCTACAGTT
Found at i:4038 original size:14 final size:14
Alignment explanation
Indices: 4019--4089 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
4009 CATCAAAGGC
4019 ATGTGGTATTTGCA
1 ATGTGGTATTTGCA
4033 ATGTGGTATTCT-CAAAA
1 ATGTGGTATT-TGC---A
* * *
4050 GCATGTGGCATTCGCG
1 --ATGTGGTATTTGCA
4066 ATGTGGTATTTGCA
1 ATGTGGTATTTGCA
4080 ATGTGGTATT
1 ATGTGGTATT
4090 CGCGACGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
14 32 0.73
15 1 0.02
17 1 0.02
19 10 0.23
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (14 bp):
ATGTGGTATTTGCA
Found at i:4048 original size:33 final size:33
Alignment explanation
Indices: 4011--4075 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
4001 TCTTCCAACA
* * *
4011 TCAAAGGCATGTGGTATTTGCAATGTGGTATTC
1 TCAAAAGCATGTGGCATTCGCAATGTGGTATTC
*
4044 TCAAAAGCATGTGGCATTCGCGATGTGGTATT
1 TCAAAAGCATGTGGCATTCGCAATGTGGTATT
4076 TGCAATGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (33 bp):
TCAAAAGCATGTGGCATTCGCAATGTGGTATTC
Found at i:4124 original size:53 final size:53
Alignment explanation
Indices: 4019--4195 Score: 249
Period size: 53 Copynumber: 3.5 Consensus size: 53
4009 CATCAAAGGC
* *
4019 ATGTGGTATTTGCAATGTGGTATT-----C-TCAAAAGCATGTGGCATTCGCG
1 ATGTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGAATGTGGCATTCGCG
* *
4066 ATGTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGAATGTGACATTCACG
1 ATGTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGAATGTGGCATTCGCG
*
4119 ATGTGGTATTTACAATGTGGTATTCGCGACGTCAAAGGAATGTGGCATTCGCG
1 ATGTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGAATGTGGCATTCGCG
* *
4172 ATATGGTATTTGCGATGTGGTATT
1 ATGTGGTATTTGCAATGTGGTATT
4196 AACGTGTAGA
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
47 24 0.21
52 1 0.01
53 89 0.78
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (53 bp):
ATGTGGTATTTGCAATGTGGTATTCGCGACGTCAAAGGAATGTGGCATTCGCG
Found at i:4168 original size:25 final size:25
Alignment explanation
Indices: 4079--4172 Score: 73
Period size: 25 Copynumber: 3.6 Consensus size: 25
4069 TGGTATTTGC
*
4079 AATGTGGTATTCGCGACGTCAAAGG
1 AATGTGGCATTCGCGACGTCAAAGG
* * * * * *
4104 AATGTGACATTCACGATGTGGTATTTA-C
1 AATGTGGCATTCGCGACGT--CA--AAGG
*
4132 AATGTGGTATTCGCGACGTCAAAGG
1 AATGTGGCATTCGCGACGTCAAAGG
4157 AATGTGGCATTCGCGA
1 AATGTGGCATTCGCGA
4173 TATGGTATTT
Statistics
Matches: 49, Mismatches: 15, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
24 1 0.02
25 30 0.61
26 1 0.02
27 1 0.02
28 15 0.31
29 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (25 bp):
AATGTGGCATTCGCGACGTCAAAGG
Found at i:4422 original size:28 final size:28
Alignment explanation
Indices: 4391--4444 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4381 CAATAACTCC
*
4391 ACAGGGTGCCACTAACACCATACTTCCA
1 ACAGGGTGCCACCAACACCATACTTCCA
* *
4419 ACAGGGTGTCGCCAACACCATACTTC
1 ACAGGGTGCCACCAACACCATACTTC
4445 TCTCCAACGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.19
Consensus pattern (28 bp):
ACAGGGTGCCACCAACACCATACTTCCA
Found at i:8140 original size:1 final size:1
Alignment explanation
Indices: 8134--8175 Score: 75
Period size: 1 Copynumber: 42.0 Consensus size: 1
8124 CATTTTGGGG
*
8134 TTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8176 CAGAAGCTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:18874 original size:21 final size:20
Alignment explanation
Indices: 18839--18878 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
18829 CAACAGCGAT
*
18839 ACAAGAACAAATTAATTCCA
1 ACAAAAACAAATTAATTCCA
18859 ACAAAAACAGAATTAATTCC
1 ACAAAAACA-AATTAATTCC
18879 TAGTCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (20 bp):
ACAAAAACAAATTAATTCCA
Found at i:19374 original size:49 final size:49
Alignment explanation
Indices: 19321--19502 Score: 282
Period size: 49 Copynumber: 3.8 Consensus size: 49
19311 TAAATTCTAC
*
19321 TCTATCTCTAGGTAATTCATCAAAATAAAGTTGATATTATACTCCTCCA
1 TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTATACTCCTCCA
*
19370 TCTATCTCTAGGTAATTCATCAAAATAAAGTTGATATTATACTCCTCCA
1 TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTATACTCCTCCA
* *
19419 TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTTCTCCA
1 TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTATACTCCTCCA
* *
19468 TC--TCTATA--TAATTCATCAAAATAAAGCTAATATTA
1 TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTA
19503 ATTGTTGCTT
Statistics
Matches: 127, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
45 25 0.20
47 5 0.04
49 97 0.76
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (49 bp):
TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTATACTCCTCCA
Found at i:26272 original size:2 final size:2
Alignment explanation
Indices: 26259--26299 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
26249 ACTACTTAAT
*
26259 AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
26300 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:26609 original size:31 final size:31
Alignment explanation
Indices: 26538--26609 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
26528 GTCTATCAGC
*
26538 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
26569 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
26599 GTTTTAATTTG
1 -TTTTAATTTG
26610 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:26882 original size:18 final size:17
Alignment explanation
Indices: 26859--26902 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
26849 ATTACAATCT
*
26859 TTATATATATTGATAATG
1 TTATATATATT-ATAATA
*
26877 TTATATTATATTATTATA
1 TTATA-TATATTATAATA
26895 TTATATAT
1 TTATATAT
26903 TATCAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
TTATATATATTATAATA
Found at i:27083 original size:12 final size:12
Alignment explanation
Indices: 27030--27085 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
27020 ATCGAAATCA
*
27030 AACCCGAGCCCG
1 AACCCGAGACCG
* *
27042 AGCCCGAGCCCG
1 AACCCGAGACCG
* *
27054 AACCTGA-ACCC
1 AACCCGAGACCG
*
27065 TACCCGAGACCG
1 AACCCGAGACCG
27077 AACCCGAGA
1 AACCCGAGA
27086 ATACCCGAAC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 7 0.21
12 27 0.79
ACGTcount: A:0.29, C:0.45, G:0.23, T:0.04
Consensus pattern (12 bp):
AACCCGAGACCG
Found at i:27095 original size:16 final size:15
Alignment explanation
Indices: 27074--27160 Score: 77
Period size: 16 Copynumber: 5.5 Consensus size: 15
27064 CTACCCGAGA
27074 CCGAACCCGAGAATAC
1 CCGAACCCGA-AATAC
*
27090 CCGAACCCGACATAAC
1 CCGAACCCGAAAT-AC
27106 CC-AAGCCCGAAAATAC
1 CCGAA-CCCG-AAATAC
**
27122 CCGAACCCGACTTAAC
1 CCGAACCCGAAAT-AC
*
27138 CCGAACCCGAAAAAAC
1 CCGAACCCG-AAATAC
27154 CCGAACC
1 CCGAACC
27161 TAAAAAAACC
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
15 6 0.10
16 46 0.79
17 6 0.10
ACGTcount: A:0.39, C:0.41, G:0.14, T:0.06
Consensus pattern (15 bp):
CCGAACCCGAAATAC
Found at i:27121 original size:32 final size:32
Alignment explanation
Indices: 27074--27160 Score: 131
Period size: 32 Copynumber: 2.7 Consensus size: 32
27064 CTACCCGAGA
*
27074 CCGAACCCGAGAATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
27106 CC-AAGCCCGAAAATACCCGAACCCGACTTAAC
1 CCGAA-CCCGAAAATACCCGAACCCGACATAAC
*
27138 CCGAACCCGAAAAAACCCGAACC
1 CCGAACCCGAAAATACCCGAACC
27161 TAAAAAAACC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 2 0.04
32 46 0.92
33 2 0.04
ACGTcount: A:0.39, C:0.41, G:0.14, T:0.06
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:27166 original size:16 final size:16
Alignment explanation
Indices: 27135--27176 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
27125 AACCCGACTT
*
27135 AACCCGAACCCGAAAA
1 AACCCGAACCCAAAAA
*
27151 AACCCGAACCTAAAAA
1 AACCCGAACCCAAAAA
*
27167 AACCTGAACC
1 AACCCGAACC
27177 GGAAGTACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.50, C:0.36, G:0.10, T:0.05
Consensus pattern (16 bp):
AACCCGAACCCAAAAA
Found at i:41872 original size:8 final size:8
Alignment explanation
Indices: 41861--41950 Score: 53
Period size: 8 Copynumber: 11.6 Consensus size: 8
41851 ATAAAAAAGT
41861 AATAGATA
1 AATAGATA
*
41869 AATAAATA
1 AATAGATA
*
41877 AATAAATA
1 AATAGATA
*
41885 GAA-AAATA
1 -AATAGATA
*
41893 AGT-GA-A
1 AATAGATA
41899 AATA-ATA
1 AATAGATA
* *
41906 GATAAATA
1 AATAGATA
*
41914 AAAAGATA
1 AATAGATA
*
41922 AATAGGTA
1 AATAGATA
*
41930 TATAGATA
1 AATAGATA
*
41938 ATTAGATA
1 AATAGATA
41946 AATAG
1 AATAG
41951 GTAGGTAAAA
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
6 4 0.06
7 6 0.10
8 50 0.81
9 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (8 bp):
AATAGATA
Found at i:42004 original size:19 final size:18
Alignment explanation
Indices: 42003--42055 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
41993 GCTAAATTAA
*
42003 TAAATAAAAAGATAAATAG
1 TAAATAAATAGAT-AATAG
42022 TAAATAAATAGATAATAG
1 TAAATAAATAGATAATAG
* *
42040 TTAAATTAATAAATAA
1 -TAAATAAATAGATAA
42056 GAATATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 5 0.17
19 25 0.83
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
TAAATAAATAGATAATAG
Found at i:42024 original size:46 final size:46
Alignment explanation
Indices: 41967--42077 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
41957 AAAAAAAAGT
*
41967 AGAT-AATAGTAAATAAATAGATTATAGCTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
* *
42012 AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAGA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
*
42058 ATATAAATAGTAAATAAATA
1 AGATAAATAGTAAATAAATA
42078 AAAAAATCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 4 0.07
46 57 0.93
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.29
Consensus pattern (46 bp):
AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
Found at i:42025 original size:27 final size:27
Alignment explanation
Indices: 41976--42036 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
41966 TAGATAATAG
* *
41976 TAAATAAATAGATTATAGCTAAATTAA
1 TAAATAAAAAGATAATAGCTAAATTAA
*
42003 TAAATAAAAAGATAAATAG-TAAATAAA
1 TAAATAAAAAGAT-AATAGCTAAATTAA
*
42030 TAGATAA
1 TAAATAA
42037 TAGTTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (27 bp):
TAAATAAAAAGATAATAGCTAAATTAA
Found at i:42052 original size:27 final size:25
Alignment explanation
Indices: 41966--42077 Score: 84
Period size: 23 Copynumber: 4.8 Consensus size: 25
41956 TAAAAAAAAG
*
41966 TAGAT-AATAGTAAATAAATAGATTA
1 TAGATAAATA-TAAATAAATAGATAA
*
41991 TAGCTAAAT-T-AATAAATA-A-AA
1 TAGATAAATATAAATAAATAGATAA
42012 -AGATAAATAGTAAATAAATAGATAA
1 TAGATAAATA-TAAATAAATAGATAA
* *
42037 TAGTTAAAT-T-AATAAATA-AGAA
1 TAGATAAATATAAATAAATAGATAA
42059 T--ATAAATAGTAAATAAATA
1 TAGATAAATA-TAAATAAATA
42078 AAAAAATCTT
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
20 12 0.17
21 1 0.01
22 7 0.10
23 32 0.45
24 3 0.04
25 6 0.08
26 10 0.14
ACGTcount: A:0.61, C:0.01, G:0.09, T:0.29
Consensus pattern (25 bp):
TAGATAAATATAAATAAATAGATAA
Found at i:54046 original size:16 final size:17
Alignment explanation
Indices: 54025--54059 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54015 CACTCCCTCC
*
54025 TAAAACT-AGAGAAAAA
1 TAAAACTAAAAGAAAAA
54041 TAAAACTAAAAGAAAAA
1 TAAAACTAAAAGAAAAA
54058 TA
1 TA
54060 GATGAAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.09, T:0.14
Consensus pattern (17 bp):
TAAAACTAAAAGAAAAA
Found at i:54592 original size:30 final size:30
Alignment explanation
Indices: 54558--54616 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
54548 CAATTCTTGC
*
54558 TTCTTGAAATAATTCTTCAAT-GATCTTCAT
1 TTCTTGAAATAA-TCTTCAATAAATCTTCAT
*
54588 TTCTTGAAATTATCTTCAATAAATCTTCA
1 TTCTTGAAATAATCTTCAATAAATCTTCA
54617 ATCACGAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (30 bp):
TTCTTGAAATAATCTTCAATAAATCTTCAT
Found at i:64257 original size:2 final size:2
Alignment explanation
Indices: 64245--64278 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
64235 GTCTCTGATT
64245 TA TA CTA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64279 ATAAACTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65296 original size:16 final size:17
Alignment explanation
Indices: 65269--65344 Score: 97
Period size: 16 Copynumber: 4.7 Consensus size: 17
65259 GTCGGGTTGA
65269 TCGGGTTCGGGTCATTT
1 TCGGGTTCGGGTCATTT
*
65286 T-GGGTTTGGGTCATTT
1 TCGGGTTCGGGTCATTT
65302 TCGGGTTCGGGTCA-TT
1 TCGGGTTCGGGTCATTT
* *
65318 T-GGATTCGGGT-AATT
1 TCGGGTTCGGGTCATTT
65333 TCGGGTTCGGGT
1 TCGGGTTCGGGT
65345 ACCCAAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.02
15 12 0.23
16 27 0.52
17 12 0.23
ACGTcount: A:0.08, C:0.13, G:0.38, T:0.41
Consensus pattern (17 bp):
TCGGGTTCGGGTCATTT
Found at i:65394 original size:17 final size:18
Alignment explanation
Indices: 65353--65394 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
65343 GTACCCAAAA
*
65353 TTTCGGGTCATTTTCTGG
1 TTTCGGGTCAGTTTCTGG
*
65371 GTT-GGGTCAGTTTC-GG
1 TTTCGGGTCAGTTTCTGG
65387 TTTCGGGT
1 TTTCGGGT
65395 TGAGCGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.20
17 14 0.70
18 2 0.10
ACGTcount: A:0.05, C:0.14, G:0.36, T:0.45
Consensus pattern (18 bp):
TTTCGGGTCAGTTTCTGG
Found at i:66288 original size:17 final size:17
Alignment explanation
Indices: 66268--66303 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66258 TTTTGTTTGA
*
66268 GCTCAGATATTGTTGGT
1 GCTCAGATATGGTTGGT
*
66285 GCTCAGTTATGGTTGGT
1 GCTCAGATATGGTTGGT
66302 GC
1 GC
66304 GGGTGTGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.33, T:0.39
Consensus pattern (17 bp):
GCTCAGATATGGTTGGT
Found at i:69820 original size:20 final size:21
Alignment explanation
Indices: 69794--69833 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
69784 CTTTCTTTAC
*
69794 TTTTTTTTTTGAATTTTCTCA
1 TTTTTTTTTTCAATTTTCTCA
69815 TTTTTTTTTTCAATTTTCT
1 TTTTTTTTTTCAATTTTCT
69834 TGGTGGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTTTTTTTCAATTTTCTCA
Found at i:71813 original size:21 final size:21
Alignment explanation
Indices: 71788--71828 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
71778 ATAGTTTTTG
*
71788 TTCAATTAAC-AATTGTCCTTT
1 TTCAAGTAACGAA-TGTCCTTT
71809 TTCAAGTAACGAATGTCCTT
1 TTCAAGTAACGAATGTCCTT
71829 GAACAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (21 bp):
TTCAAGTAACGAATGTCCTTT
Found at i:72214 original size:6 final size:6
Alignment explanation
Indices: 72198--72239 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
72188 AAAGTTAAGA
72198 AAAACAC AAAAAC AAAAAAC AAAAAC AAAATAC -AAAAC AAAA
1 AAAA-AC AAAAAC -AAAAAC AAAAAC AAAA-AC AAAAAC AAAA
72240 CTAAACTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 2 0.06
6 18 0.56
7 12 0.38
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:72215 original size:7 final size:7
Alignment explanation
Indices: 72197--72234 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
72187 CAAAGTTAAG
72197 AAAAACA
1 AAAAACA
72204 CAAAAACA
1 -AAAAACA
72212 AAAAAC-
1 AAAAACA
72218 AAAAACA
1 AAAAACA
*
72225 AAATACA
1 AAAAACA
72232 AAA
1 AAA
72235 CAAAACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 6 0.21
7 15 0.54
8 7 0.25
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAAACA
Found at i:72219 original size:13 final size:13
Alignment explanation
Indices: 72197--72239 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
72187 CAAAGTTAAG
72197 AAAAACACAAAAAC
1 AAAAA-ACAAAAAC
72211 AAAAAACAAAAAC
1 AAAAAACAAAAAC
*
72224 AAAATAC-AAAAC
1 AAAAAACAAAAAC
72236 AAAA
1 AAAA
72240 CTAAACTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 9 0.32
13 14 0.50
14 5 0.18
ACGTcount: A:0.81, C:0.16, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:74475 original size:21 final size:21
Alignment explanation
Indices: 74450--74491 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
74440 TATGTTGAGA
74450 TGCATTCATGTGGGATTGTTG
1 TGCATTCATGTGGGATTGTTG
74471 TGCATTCATGTGGGATTGTTG
1 TGCATTCATGTGGGATTGTTG
74492 CTAAAGATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (21 bp):
TGCATTCATGTGGGATTGTTG
Found at i:76737 original size:25 final size:25
Alignment explanation
Indices: 76709--76762 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
76699 TTTAATATAT
*
76709 TTTAAGATTT-AAAAACTATATTTAA
1 TTTAAGATTTGAAAAA-TATAATTAA
76734 TTTAAGATTTGAAAAATATAATTAA
1 TTTAAGATTTGAAAAATATAATTAA
76759 TTTA
1 TTTA
76763 TTTAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (25 bp):
TTTAAGATTTGAAAAATATAATTAA
Found at i:76773 original size:22 final size:22
Alignment explanation
Indices: 76740--76790 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
76730 TTAATTTAAG
76740 ATTTGAAAAAT-ATAATTA-ATTT
1 ATTT-AAAAATAAT-ATTATATTT
*
76762 ATTTAAATAATAATTTTATATTT
1 ATTTAAA-AATAATATTATATTT
76785 ATTTAA
1 ATTTAA
76791 TCCTTTCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 3 0.12
22 10 0.40
23 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTAAAAATAATATTATATTT
Found at i:77820 original size:19 final size:20
Alignment explanation
Indices: 77798--77838 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
77788 TTAAAAAGTG
77798 TTTGTGATTTT-TATTTAAT
1 TTTGTGATTTTATATTTAAT
*
77817 TTTGTGATTTTATTTTTAAT
1 TTTGTGATTTTATATTTAAT
77837 TT
1 TT
77839 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.71
Consensus pattern (20 bp):
TTTGTGATTTTATATTTAAT
Found at i:80728 original size:13 final size:13
Alignment explanation
Indices: 80710--80745 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
80700 GTTTCAAATA
80710 TAGTATATATAAG
1 TAGTATATATAAG
*
80723 TAGTATATATATG
1 TAGTATATATAAG
80736 TA-TATATATA
1 TAGTATATATA
80746 CTAGTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (13 bp):
TAGTATATATAAG
Found at i:80891 original size:22 final size:22
Alignment explanation
Indices: 80866--81014 Score: 72
Period size: 22 Copynumber: 6.8 Consensus size: 22
80856 ATGATCTCCT
80866 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACATTCC
** *
80888 TATGAAATTTCAATAACGA-TAC
1 TATGAAATTTTGATAAC-ATTCC
* * * * **
80910 TAAGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACATTCC
** * *
80932 TAT-AAATTTTTTTTAACTTTCT
1 TATGAAA-TTTTGATAACATTCC
* *
80954 TATGAAATTTTGTTAACCTTCC
1 TATGAAATTTTGATAACATTCC
* * *
80976 TAAGGAATTTTGA-AGAC-CTCAC
1 TATGAAATTTTGATA-ACATTC-C
80998 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
81015 TAACACTATG
Statistics
Matches: 93, Mismatches: 27, Indels: 14
0.69 0.20 0.10
Matches are distributed among these distances:
21 5 0.05
22 83 0.89
23 5 0.05
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACATTCC
Found at i:81015 original size:66 final size:66
Alignment explanation
Indices: 80866--81015 Score: 151
Period size: 66 Copynumber: 2.3 Consensus size: 66
80856 ATGATCTCCT
* * **
80866 TATGAAATTTTGATAACATTCCTATGAAATTTCAATAACGATACTAAGGAATTTTGAGAACCTTT
1 TATGAAATTTTGATAACTTTCCTATGAAATTTCAATAACCATACTAAGGAATTTTGAGAACCTCA
*
80931 T
66 C
** * *** * *
80932 TAT-AAATTTTTTTTAACTTTCTTATGAAATTTTGTTAACCTTCCTAAGGAATTTTGA-AGACCT
1 TATGAAA-TTTTGATAACTTTCCTATGAAATTTCAATAACCATACTAAGGAATTTTGAGA-ACCT
80995 CAC
64 CAC
80998 TATGAAATTTTGATAACT
1 TATGAAATTTTGATAACT
81016 AACACTATGA
Statistics
Matches: 66, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
65 4 0.06
66 59 0.89
67 3 0.05
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (66 bp):
TATGAAATTTTGATAACTTTCCTATGAAATTTCAATAACCATACTAAGGAATTTTGAGAACCTCA
C
Found at i:83932 original size:15 final size:17
Alignment explanation
Indices: 83905--83943 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
83895 CAATTTAGCA
83905 TGCTTTTGGTTTGT-TT
1 TGCTTTTGGTTTGTGTT
*
83921 TG-TTTTGTTTTGTGTT
1 TGCTTTTGGTTTGTGTT
83937 TGCTTTT
1 TGCTTTT
83944 CCTGTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 10 0.50
16 6 0.30
17 4 0.20
ACGTcount: A:0.00, C:0.05, G:0.23, T:0.72
Consensus pattern (17 bp):
TGCTTTTGGTTTGTGTT
Found at i:87546 original size:40 final size:41
Alignment explanation
Indices: 87466--87547 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
87456 AAAAATAGTT
*
87466 TTATGAGTCCTTGAACCCAACAAGTTTTGAAGTGATGTAAA
1 TTATGAGTCCTTAAACCCAACAAGTTTTGAAGTGATGTAAA
87507 TTATGAGTCCTTAAACCCAACAAG-TTTGAAGTGATGTAAA
1 TTATGAGTCCTTAAACCCAACAAGTTTTGAAGTGATGTAAA
87547 T
1 T
87548 ATAATAATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (41 bp):
TTATGAGTCCTTAAACCCAACAAGTTTTGAAGTGATGTAAA
Found at i:90849 original size:2 final size:2
Alignment explanation
Indices: 90844--90883 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
90834 TTTTAACTAG
90844 AT AT AT AT AT 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
90884 TACGGTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95827 original size:19 final size:19
Alignment explanation
Indices: 95796--95843 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
95786 CTATTAGGGT
95796 TTAATTAATTAATGTTATT-A
1 TTAATT-ATTAATGTT-TTCA
*
95816 TTATTTATTAATGTTTTCA
1 TTAATTATTAATGTTTTCA
95835 TTAATTATT
1 TTAATTATT
95844 TCCTTAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
TTAATTATTAATGTTTTCA
Found at i:110133 original size:51 final size:51
Alignment explanation
Indices: 110073--110171 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
110063 ATTACAGAAG
110073 TGTAATATTATTTTGCTTGATGCCTTTACATTATACAAAATTTTCCATAAA
1 TGTAATATTATTTTGCTTGATGCCTTTACATTATACAAAATTTTCCATAAA
*
110124 TGTAATATTATTTTGCTTGATGCCTTTACATTATACAAATTTTTCCAT
1 TGTAATATTATTTTGCTTGATGCCTTTACATTATACAAAATTTTCCAT
110172 TTTTAGTTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.47
Consensus pattern (51 bp):
TGTAATATTATTTTGCTTGATGCCTTTACATTATACAAAATTTTCCATAAA
Done.