Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012538.1 Corchorus olitorius cultivar O-4 contig12571, 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: 57872
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:2862 original size:28 final size:28
Alignment explanation
Indices: 2825--3046 Score: 148
Period size: 28 Copynumber: 8.0 Consensus size: 28
2815 TATCTCCGAG
* * * *
2825 AGCATGCTACCGTTTTGCGGTCTTTGGA
1 AGCATACTACCGCTTCGCGATCTTTGGA
* * *
2853 AGCATACTACCCCTTCGCGATCTCTGGG
1 AGCATACTACCGCTTCGCGATCTTTGGA
* * * *
2881 AGCGTACTACCGCTTTGCAATCTTTGGC
1 AGCATACTACCGCTTCGCGATCTTTGGA
* * *
2909 TGCGTACTACCGCTTCGCGATCTTTGGG
1 AGCATACTACCGCTTCGCGATCTTTGGA
* * *
2937 GGCGTACT-CCTACTTCGCGATCTTTGGGA
1 AGCATACTACC-GCTTCGCGATCTTT-GGA
* *
2966 TG--TACTACCGCTTCGCGATCTTTGGG
1 AGCATACTACCGCTTCGCGATCTTTGGA
* * * *
2992 AGAATACTTCCAG-TTTGCGGTCTTTGGGA
1 AGCATACTACC-GCTTCGCGATCTTT-GGA
* *
3021 A-TATACTACCGCTTCGTGATCTTTGG
1 AGCATACTACCGCTTCGCGATCTTTGG
3047 GGGCGCACGA
Statistics
Matches: 153, Mismatches: 33, Indels: 17
0.75 0.16 0.08
Matches are distributed among these distances:
26 3 0.02
27 22 0.14
28 121 0.79
29 7 0.05
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (28 bp):
AGCATACTACCGCTTCGCGATCTTTGGA
Found at i:2905 original size:56 final size:55
Alignment explanation
Indices: 2831--3047 Score: 199
Period size: 56 Copynumber: 3.9 Consensus size: 55
2821 CGAGAGCATG
* * * * *
2831 CTACCGTTTTGCGGTCTTTGGAAGCATACTACCCCTTCGCGATCTCTGGGAGCGTA
1 CTACCGCTTTGCGATCTTTGGATGC-TACTACCGCTTCGCGATCTTTGGGAGCGTA
* * *
2887 CTACCGCTTTGCAATCTTTGGCTGCGTACTACCGCTTCGCGATCTTTGGGGGCGTA
1 CTACCGCTTTGCGATCTTTGGATGC-TACTACCGCTTCGCGATCTTTGGGAGCGTA
* * **
2943 CT-CCTACTTCGCGATCTTTGGGATG-TACTACCGCTTCGCGATCTTTGGGAGAATA
1 CTACC-GCTTTGCGATCTTT-GGATGCTACTACCGCTTCGCGATCTTTGGGAGCGTA
* * * *
2998 CTTCCAG-TTTGCGGTCTTTGGGAAT-ATACTACCGCTTCGTGATCTTTGGG
1 CTACC-GCTTTGCGATCTTT-GG-ATGCTACTACCGCTTCGCGATCTTTGGG
3048 GGCGCACGAC
Statistics
Matches: 135, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
55 44 0.33
56 87 0.64
57 4 0.03
ACGTcount: A:0.15, C:0.26, G:0.25, T:0.33
Consensus pattern (55 bp):
CTACCGCTTTGCGATCTTTGGATGCTACTACCGCTTCGCGATCTTTGGGAGCGTA
Found at i:3100 original size:29 final size:29
Alignment explanation
Indices: 3068--3418 Score: 216
Period size: 29 Copynumber: 12.3 Consensus size: 29
3058 GCCATCTTTC
* *
3068 GATGGTGGGTGTGCGGCACCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * * ***
3097 GATGGTGGGAGCATGGCGCCCT-TT-TTT
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * *
3124 TATGGTGGGCGTGTA--GCGCACTCTTCCGA
1 GATGGT-GG-GTGTACGGCGCCCTCTTCCAA
* *
3153 GATGGTGGCTATACGGCGCCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * *
3182 GATGGTAGGCGTACGACGCCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * *
3211 GATTGTGGCTGTTC--C-CCAC-C-TCCAA
1 GATGGTGGGTGTACGGCGCC-CTCTTCCAA
* *
3236 GATGGTGGCTGTACAGCGCCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * *
3265 GATGGTGGGTGTATGACACCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * **
3294 GATGGTGGGCGTACCGCGCCCTCTTTTAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * * *
3323 GATGGTGGCTGTACGACACCCTCTTCCAT
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * * * *
3352 GTTAGTAGCTGTACAGCGCCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
* * * ** * *
3381 CATGGCGGCTACACTGCACCCTCTTCCAA
1 GATGGTGGGTGTACGGCGCCCTCTTCCAA
3410 GATGGTGGG
1 GATGGTGGG
3419 CGCGCTCCCA
Statistics
Matches: 239, Mismatches: 71, Indels: 24
0.72 0.21 0.07
Matches are distributed among these distances:
25 17 0.07
26 3 0.01
27 18 0.08
28 11 0.05
29 190 0.79
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.26
Consensus pattern (29 bp):
GATGGTGGGTGTACGGCGCCCTCTTCCAA
Found at i:3208 original size:58 final size:58
Alignment explanation
Indices: 3138--3420 Score: 269
Period size: 58 Copynumber: 4.9 Consensus size: 58
3128 GTGGGCGTGT
* * * * *
3138 AGCGCACTCTTCCGAGATGGTGGCTATACGGCGCCCTCTTCCAAGATGGTAGGCGTAC
1 AGCGCCCTCTTCCAAGATGGTGGCTGTACGACACCCTCTTCCAAGATGGTAGGCGTAC
* *
3196 -GACGCCCTCTTCCAAGATTGTGGCTGTTC--C-CCAC-C-TCCAAGATGGT-GGCTGTAC
1 AG-CGCCCTCTTCCAAGATGGTGGCTGTACGACACC-CTCTTCCAAGATGGTAGGC-GTAC
* * *
3250 AGCGCCCTCTTCCAAGATGGTGGGTGTATGACACCCTCTTCCAAGATGGTGGGCGTAC
1 AGCGCCCTCTTCCAAGATGGTGGCTGTACGACACCCTCTTCCAAGATGGTAGGCGTAC
* ** * * *
3308 CGCGCCCTCTTTTAAGATGGTGGCTGTACGACACCCTCTTCCATGTTAGTA-GCTGTAC
1 AGCGCCCTCTTCCAAGATGGTGGCTGTACGACACCCTCTTCCAAGATGGTAGGC-GTAC
* * ** *
3366 AGCGCCCTCTTCCAACATGGCGGCTACACTG-CACCCTCTTCCAAGATGGTGGGCG
1 AGCGCCCTCTTCCAAGATGGTGGCTGTAC-GACACCCTCTTCCAAGATGGTAGGCG
3421 CGCTCCCACT
Statistics
Matches: 183, Mismatches: 29, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
53 3 0.02
54 38 0.21
55 4 0.02
56 4 0.02
57 6 0.03
58 122 0.67
59 6 0.03
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.25
Consensus pattern (58 bp):
AGCGCCCTCTTCCAAGATGGTGGCTGTACGACACCCTCTTCCAAGATGGTAGGCGTAC
Found at i:3268 original size:112 final size:115
Alignment explanation
Indices: 3138--3420 Score: 324
Period size: 112 Copynumber: 2.5 Consensus size: 115
3128 GTGGGCGTGT
* * * *
3138 AGCGCACTCTTCCGAGATGGTGGCTATACGGCGCCCTCTTCCAAGATGGTAGGCGTA-CGACGCC
1 AGCGCCCTCTTCCAAGATGGTGGCTATACGGCACCCTCTTCCAAGATGGTGGGCGTACCG-CGCC
* * * *
3202 CTCTTCCAAGATTGTGGCTGTTC-C-CCAC-C-TCCAAGATGGTGGCTGTAC
65 CTCTTCCAAGATGGTGGCTGTACACACC-CTCTTCCAAGATAGTAGCTGTAC
* * * *
3250 AGCGCCCTCTTCCAAGATGGTGGGTGTATGACACCCTCTTCCAAGATGGTGGGCGTACCGCGCCC
1 AGCGCCCTCTTCCAAGATGGTGGCTATACGGCACCCTCTTCCAAGATGGTGGGCGTACCGCGCCC
** * *
3315 TCTTTTAAGATGGTGGCTGTACGACACCCTCTTCCATGTTAGTAGCTGTAC
66 TCTTCCAAGATGGTGGCTGTAC-ACACCCTCTTCCAAGATAGTAGCTGTAC
* * * *
3366 AGCGCCCTCTTCCAACATGGCGGCTACACTGCACCCTCTTCCAAGATGGTGGGCG
1 AGCGCCCTCTTCCAAGATGGTGGCTATACGGCACCCTCTTCCAAGATGGTGGGCG
3421 CGCTCCCACT
Statistics
Matches: 141, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
112 72 0.51
113 2 0.01
114 2 0.01
115 3 0.02
116 62 0.44
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.25
Consensus pattern (115 bp):
AGCGCCCTCTTCCAAGATGGTGGCTATACGGCACCCTCTTCCAAGATGGTGGGCGTACCGCGCCC
TCTTCCAAGATGGTGGCTGTACACACCCTCTTCCAAGATAGTAGCTGTAC
Found at i:3612 original size:28 final size:28
Alignment explanation
Indices: 3580--3830 Score: 215
Period size: 28 Copynumber: 9.0 Consensus size: 28
3570 TTCGAATTTC
* *
3580 GAGGGCGTACTACCATTTCGCAATCTTG
1 GAGGGCGTACTACCACTTCGCGATCTTG
* * * **
3608 GAGGGTGTACTACCAATTGGCGGCCTTTG
1 GAGGGCGTACTACCACTTCGCGATC-TTG
* *
3637 G-GAGCGTACTACCGCTTCGC-ACTCTT-
1 GAGGGCGTACTACCACTTCGCGA-TCTTG
* * * *
3663 TATGAGG-GTACTACCGCTTCACGCTCTT-
1 GA-G-GGCGTACTACCACTTCGCGATCTTG
* * * *
3691 TATGAGCGTACTACCTCTTCGCGAGCTTG
1 GA-GGGCGTACTACCACTTCGCGATCTTG
* *
3720 GAGGGCGTACTACCACTTCGTGAGCTTG
1 GAGGGCGTACTACCACTTCGCGATCTTG
* *
3748 GAGGGCGTACTACCACTTCGTGAGCTTG
1 GAGGGCGTACTACCACTTCGCGATCTTG
*
3776 GAGGGCGTACTACCACTTCGCTATCTTG
1 GAGGGCGTACTACCACTTCGCGATCTTG
*
3804 GAGGGCGTACTACCACTTCGTGATCTT
1 GAGGGCGTACTACCACTTCGCGATCTT
3831 TGGGGGTGCA
Statistics
Matches: 184, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
27 3 0.02
28 175 0.95
29 6 0.03
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (28 bp):
GAGGGCGTACTACCACTTCGCGATCTTG
Found at i:3848 original size:56 final size:56
Alignment explanation
Indices: 3696--3858 Score: 195
Period size: 56 Copynumber: 2.9 Consensus size: 56
3686 CTCTTTATGA
* * * ** *
3696 GCGTACTACCTCTTCGCGAGCTTGGAGGGCGTACTACCACTTCGTGAGCTTGGAGG
1 GCGTACTACCACTTCGTGAGCTTGGAGGGCGCACTACCACTTCGCAATCTTGGAGG
* *
3752 GCGTACTACCACTTCGTGAGCTTGGAGGGCGTACTACCACTTCGCTATCTTGGAGG
1 GCGTACTACCACTTCGTGAGCTTGGAGGGCGCACTACCACTTCGCAATCTTGGAGG
* * *
3808 GCGTACTACCACTTCGTGATCTTTGG-GGGTGCA-TGCCCACTTCGCAATCTT
1 GCGTACTACCACTTCGTGAGC-TTGGAGGGCGCACT-ACCACTTCGCAATCTT
3859 TGGGCATTCT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 1 0.01
56 90 0.95
57 4 0.04
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (56 bp):
GCGTACTACCACTTCGTGAGCTTGGAGGGCGCACTACCACTTCGCAATCTTGGAGG
Found at i:3966 original size:26 final size:25
Alignment explanation
Indices: 3911--3967 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
3901 CAAATTTCGA
* *
3911 GGGCGCTCTACCCTTTTCGGACTTG
1 GGGCGTTCTACCCTTTTCGAACTTG
3936 GGGCGTTCTACGCCTTTT-GAACTTG
1 GGGCGTTCTAC-CCTTTTCGAACTTG
3961 GAGGCGT
1 G-GGCGT
3968 CCTATGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.11, C:0.26, G:0.32, T:0.32
Consensus pattern (25 bp):
GGGCGTTCTACCCTTTTCGAACTTG
Found at i:3978 original size:26 final size:25
Alignment explanation
Indices: 3931--3980 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3921 CCCTTTTCGG
* *
3931 ACTTGGGGCGTTCTACGCCTTTTGA
1 ACTTGGGGCGTCCTACGACTTTTGA
*
3956 ACTTGGAGGCGTCCTATGACTTTTG
1 ACTTGG-GGCGTCCTACGACTTTTG
3981 CGCGTGCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (25 bp):
ACTTGGGGCGTCCTACGACTTTTGA
Found at i:5953 original size:14 final size:15
Alignment explanation
Indices: 5917--5948 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5907 TTAGTTGGAT
*
5917 TTAAATTTTTTATAA
1 TTAAATTTTTAATAA
5932 TTAAATTTTTAATAA
1 TTAAATTTTTAATAA
5947 TT
1 TT
5949 TATTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAAATTTTTAATAA
Found at i:6813 original size:16 final size:16
Alignment explanation
Indices: 6792--6824 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6782 GGTTTAGCCT
6792 TCGGGTCATCC-GGGTC
1 TCGGGTCA-CCTGGGTC
6808 TCGGGTCACCTGGGTC
1 TCGGGTCACCTGGGTC
6824 T
1 T
6825 AGGATTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.06, C:0.30, G:0.36, T:0.27
Consensus pattern (16 bp):
TCGGGTCACCTGGGTC
Found at i:15525 original size:27 final size:27
Alignment explanation
Indices: 15477--15534 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
15467 AGTTTGGTGT
** * * *
15477 AGTTTGGTGTTGTTAAGGAGTAGGAAC
1 AGTTTGGTAATGTAAAGAAGTAGGAAA
15504 AGTTTGGTAATGTAAAGAAGTAGGAAA
1 AGTTTGGTAATGTAAAGAAGTAGGAAA
15531 AGTT
1 AGTT
15535 GAGTAGCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.33, T:0.31
Consensus pattern (27 bp):
AGTTTGGTAATGTAAAGAAGTAGGAAA
Found at i:20608 original size:6 final size:6
Alignment explanation
Indices: 20597--20624 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20587 TATAGTAAAA
20597 AAATCC AAATCC AAATCC AAATCC AAAT
1 AAATCC AAATCC AAATCC AAATCC AAAT
20625 GAAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCC
Found at i:25282 original size:22 final size:22
Alignment explanation
Indices: 25233--25284 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
25223 AAATATTACC
* **
25233 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
25255 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
25278 A-AATTAT
1 ATAATTAT
25285 GGAATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:26264 original size:7 final size:7
Alignment explanation
Indices: 26252--26322 Score: 58
Period size: 7 Copynumber: 10.3 Consensus size: 7
26242 TAACGTGTTT
26252 TTTTTTC
1 TTTTTTC
26259 TTTTTTC
1 TTTTTTC
*
26266 -TTATTC
1 TTTTTTC
26272 TTTTATTC
1 TTTT-TTC
*
26280 TTTATTC
1 TTTTTTC
**
26287 TTTTTAG
1 TTTTTTC
26294 TTTTTTC
1 TTTTTTC
*
26301 --TCTTC
1 TTTTTTC
26306 TTTTTTC
1 TTTTTTC
26313 TTTCTTTC
1 TTT-TTTC
26321 TT
1 TT
26323 CCTCCCGCAC
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
5 4 0.08
6 5 0.10
7 28 0.57
8 12 0.24
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:26286 original size:15 final size:13
Alignment explanation
Indices: 26256--26291 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
26246 GTGTTTTTTT
26256 TTCTTTTTTCTTA
1 TTCTTTTTTCTTA
26269 TTCTTTTATTCTTTA
1 TTCTTTT-TTC-TTA
26284 TTCTTTTT
1 TTCTTTTT
26292 AGTTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.33
14 4 0.19
15 10 0.48
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTTTCTTA
Found at i:26311 original size:12 final size:11
Alignment explanation
Indices: 26249--26319 Score: 56
Period size: 12 Copynumber: 6.3 Consensus size: 11
26239 AAGTAACGTG
26249 TTTTTT-TTTC
1 TTTTTTCTTTC
26259 TTTTTTCTTATTC
1 TTTTTTC-T-TTC
*
26272 TTTTATTCTTTA
1 TTTT-TTCTTTC
* **
26284 TTCTTT-TTAG
1 TTTTTTCTTTC
26294 TTTTTTCTCTTC
1 TTTTTTCT-TTC
26306 TTTTTTCTTTC
1 TTTTTTCTTTC
26317 TTT
1 TTT
26320 CTTCCTCCCG
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
10 13 0.27
11 9 0.19
12 15 0.31
13 8 0.17
14 3 0.06
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:27211 original size:23 final size:25
Alignment explanation
Indices: 27166--27219 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
27156 AATCTTTGAA
*
27166 TTTGCTGGTTATTTTTTCATTTTAT
1 TTTGCTGGTAATTTTTTCATTTTAT
* *
27191 TTTGCTGG-AATTTTTT-TTTTTTT
1 TTTGCTGGTAATTTTTTCATTTTAT
27214 TTTGCT
1 TTTGCT
27220 CTTATTGGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 7 0.27
25 8 0.31
ACGTcount: A:0.09, C:0.07, G:0.13, T:0.70
Consensus pattern (25 bp):
TTTGCTGGTAATTTTTTCATTTTAT
Found at i:40680 original size:19 final size:19
Alignment explanation
Indices: 40656--40702 Score: 80
Period size: 17 Copynumber: 2.6 Consensus size: 19
40646 ACACTCTCAC
40656 AACTCAAAATGTTAATTGA
1 AACTCAAAATGTTAATTGA
40675 AACTCAAAA--TTAATTGA
1 AACTCAAAATGTTAATTGA
40692 AACTCAAAATG
1 AACTCAAAATG
40703 AATTAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 17 0.65
19 9 0.35
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.28
Consensus pattern (19 bp):
AACTCAAAATGTTAATTGA
Found at i:41130 original size:13 final size:13
Alignment explanation
Indices: 41112--41136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41102 ATTTTTTCAT
41112 TTTTTTGAATTTA
1 TTTTTTGAATTTA
41125 TTTTTTGAATTT
1 TTTTTTGAATTT
41137 TGTTAATTAT
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTTTGAATTTA
Found at i:41147 original size:21 final size:22
Alignment explanation
Indices: 41098--41144 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
41088 TAGTTGCTTC
* *
41098 ATTTATTTTTTCATTTTTTTGA
1 ATTTATTTTTTAATTTTGTTGA
41120 ATTTATTTTTTGAATTTTGTT-A
1 ATTTATTTTTT-AATTTTGTTGA
41142 ATT
1 ATT
41145 ATTAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.70
Consensus pattern (22 bp):
ATTTATTTTTTAATTTTGTTGA
Found at i:41697 original size:16 final size:15
Alignment explanation
Indices: 41676--41741 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 15
41666 AGTCAACTTT
41676 TCGGGTCATTCGGGTC
1 TCGGGTCA-TCGGGTC
*
41692 TCGGGTCACACGGGTC
1 TCGGGTCA-TCGGGTC
41708 TCGGGTCATCTGGGT-
1 TCGGGTCATC-GGGTC
41723 TCTGGGTCAGTCGGGTC
1 TC-GGGTCA-TCGGGTC
41740 TC
1 TC
41742 AGGTTGTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.07
16 36 0.84
17 4 0.09
ACGTcount: A:0.08, C:0.26, G:0.38, T:0.29
Consensus pattern (15 bp):
TCGGGTCATCGGGTC
Found at i:41713 original size:32 final size:32
Alignment explanation
Indices: 41676--41741 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
41666 AGTCAACTTT
41676 TCGGGTCAT-TCGGG-TCTCGGGTCACACGGGTC
1 TCGGGTCATCT-GGGTTCT-GGGTCACACGGGTC
**
41708 TCGGGTCATCTGGGTTCTGGGTCAGTCGGGTC
1 TCGGGTCATCTGGGTTCTGGGTCACACGGGTC
41740 TC
1 TC
41742 AGGTTGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 26 0.87
33 4 0.13
ACGTcount: A:0.08, C:0.26, G:0.38, T:0.29
Consensus pattern (32 bp):
TCGGGTCATCTGGGTTCTGGGTCACACGGGTC
Found at i:43120 original size:444 final size:430
Alignment explanation
Indices: 42390--43304 Score: 1139
Period size: 444 Copynumber: 2.1 Consensus size: 430
42380 GTGGGTCCCA
* * * **
42390 ATCTCCACCAACAACCA-ATTTT-TTT-GATTATTTATCAAATGATTCTCATACTTTTCTCATTT
1 ATCTCCATCAACAAACATTTTTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTCATTT
* * * * * *
42452 ATGCTATTTAATCCTTTACTTATTCTGTCTTAATCGATTTAACGATTCGATTTTAATTGTTTTTT
66 ATACTACTTAATCCTTTACTTATTATATCTTAATCGATTAAACGATTCGACTTTAATTGTTTTTT
*
42517 TTCTATATTTCCGATTAAGGTTATTCAAATGTCCATTAAAAGGTAATTTTATGATCTACTACTTT
131 TTCTATATTTCCGATTAAGGTGATTCAAATGTCCATTAAAAGGTAATTTTATGATCTACTACTTT
* * *
42582 CATGAAGGACTCAAAAGCTAATTTTTATGTTTCAGCTCTAAAAGATGCTTCTAAAATTTGGTGGT
196 CATGAAGGACTCAAAAGCCAATTTTTATGTTTCAACTCTAAAAAATGCTTCTAAAATTTGGTGGT
* * * * * *
42647 TTCAATTGCCGGTCTATTTGATTTCATATAA-TTTTCGACCCACATATCCTATTGAAGTTATTGA
261 TTCAATTGCCGGTCTATTTAATATCATATAACTTTT-GACCCACAAATCCGATTGAAGTTACTCA
* *
42711 AGTGTCAGTTAAAAGGTTATTGCATGATCTACGACTTTCATGAAGGACCTGAAAGTTGAATTTGA
325 AGT-TCAGTTAAAAGG-TATTGCATGATCTACGACTTTCATGAAGGACCCGAAA-CTGAATTTGA
* *
42776 TTGACAAGTTTCATGAAGGGCTCAAGAGGAAA-TTTTATATTTC
387 TCGACAAGTTTCATGAAAGGCTCAAGAGGAAATTTTTATATTTC
*
42819 ATCTCCATCAACAAACATTTTTTATTTGGATTATTTATCAATTGACCCTCATACTTTTCT-ATTT
1 ATCTCCATCAACAAACATTTTTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTCATTT
* * *
42883 CATACTACTTAATCCTTTA-TTAATTATATCTTAATCGATTAAACGCTTC-AGCTTTATTTTTTA
66 -ATACTACTTAATCCTTTACTT-ATTATATCTTAATCGATTAAACGATTCGA-CTTTAATTGTT-
* * * *
42946 TTTTTTGTTATATTTGTCCGTTTAAGGTGATTCAGATGTCTATTAAAAGGT-ATTTTCATGATCT
127 TTTTTT-CTATA-TT-TCCGATTAAGGTGATTCAAATGTCCATTAAAAGGTAATTTT-ATGATCT
* * *
43010 GCAAGACTACAACTTTCATTAAGGACTCACAATCCAATTTTTATGTTTCAACTCTAAAAAATGCT
188 -----ACT---ACTTTCATGAAGGACTCAAAAGCCAATTTTTATGTTTCAACTCTAAAAAATGCT
* * * *
43075 TCTGAAATTTGGTGGTTTCGATTGCCGGTCTATTTAATATCATATAACTTTTGATCCAGAAATCC
245 TCTAAAATTTGGTGGTTTCAATTGCCGGTCTATTTAATATCATATAACTTTTGACCCACAAATCC
*
43140 GATTGAAGTTACTCAAGTTCAGTTAAAAGGTATTGCATGATTTACGACTTTCATGAAGGACCCGA
310 GATTGAAGTTACTCAAGTTCAGTTAAAAGGTATTGCATGATCTACGACTTTCATGAAGGACCCGA
* * * * *
43205 TACTGAATTTGATCGACGAGTTTCATGAAAGGTTTAAGAGGAAATTTTTATGTTTC
375 AACTGAATTTGATCGACAAGTTTCATGAAAGGCTCAAGAGGAAATTTTTATATTTC
* *
43261 GTAT-CATCAACAAACAATTTTTTATTTGGATTATTTATCAAATG
1 ATCTCCATCAACAAAC-ATTTTTTATTTGGATTATTTATCAAATG
43305 GTCACTTTAG
Statistics
Matches: 415, Mismatches: 49, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
429 15 0.04
430 4 0.01
431 10 0.02
432 76 0.18
433 6 0.01
434 4 0.01
435 7 0.02
436 38 0.09
441 50 0.12
442 73 0.18
443 12 0.03
444 116 0.28
445 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (430 bp):
ATCTCCATCAACAAACATTTTTTATTTGGATTATTTATCAAATGACCCTCATACTTTTCTCATTT
ATACTACTTAATCCTTTACTTATTATATCTTAATCGATTAAACGATTCGACTTTAATTGTTTTTT
TTCTATATTTCCGATTAAGGTGATTCAAATGTCCATTAAAAGGTAATTTTATGATCTACTACTTT
CATGAAGGACTCAAAAGCCAATTTTTATGTTTCAACTCTAAAAAATGCTTCTAAAATTTGGTGGT
TTCAATTGCCGGTCTATTTAATATCATATAACTTTTGACCCACAAATCCGATTGAAGTTACTCAA
GTTCAGTTAAAAGGTATTGCATGATCTACGACTTTCATGAAGGACCCGAAACTGAATTTGATCGA
CAAGTTTCATGAAAGGCTCAAGAGGAAATTTTTATATTTC
Found at i:48556 original size:13 final size:13
Alignment explanation
Indices: 48538--48563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48528 GCTGGGTATG
48538 CTGCTAAGTAGAT
1 CTGCTAAGTAGAT
48551 CTGCTAAGTAGAT
1 CTGCTAAGTAGAT
48564 GCAATCGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
CTGCTAAGTAGAT
Found at i:50749 original size:1 final size:1
Alignment explanation
Indices: 50714--50738 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
50704 GAAAGATTAG
50714 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
50739 GGCAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:54554 original size:23 final size:23
Alignment explanation
Indices: 54524--54572 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
54514 AAATGGTGTT
*
54524 ATACGTTGTACATGCTCTAAGCA
1 ATACGTTGTACATACTCTAAGCA
54547 ATACGTTGTACATACTCTAAGCA
1 ATACGTTGTACATACTCTAAGCA
54570 ATA
1 ATA
54573 GAAACACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (23 bp):
ATACGTTGTACATACTCTAAGCA
Found at i:54616 original size:137 final size:138
Alignment explanation
Indices: 54435--54683 Score: 421
Period size: 137 Copynumber: 1.8 Consensus size: 138
54425 GTTTTGGTGT
** *
54435 GAAACACATTGGAGTGAAAAAAATATTTGATGTAAGTATATTCCAAAAAGATTCCATTTTAACAC
1 GAAACACATTAAAGTGAAAAAAATATTTGATGTAAGCATATTCCAAAAAGATTCCATTTTAACAC
*
54500 CAAAATGGTGCAAAAAATGGTGTTATACGTTGTACATGCTCTAAGCAATACGTTGTACATACTCT
66 CAAAATGATGCAAAAAATGGTGTTATACGTTGTACATGCTCTAAGCAATACGTTGTACATACTCT
54565 AAGCAATA
131 AAGCAATA
*
54573 GAAACACATTAAAGTG-AAAAAATATTT-AGTGTAAGCATATTCCAAAAAGATTTCATTTTAACA
1 GAAACACATTAAAGTGAAAAAAATATTTGA-TGTAAGCATATTCCAAAAAGATTCCATTTTAACA
*
54636 CCAAAATGATGCAAAAATTGGTGTTATACGTTGTACATGCTCTAAGCA
65 CCAAAATGATGCAAAAAATGGTGTTATACGTTGTACATGCTCTAAGCA
54684 GTAGAACCAA
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
136 1 0.01
137 89 0.86
138 14 0.13
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.29
Consensus pattern (138 bp):
GAAACACATTAAAGTGAAAAAAATATTTGATGTAAGCATATTCCAAAAAGATTCCATTTTAACAC
CAAAATGATGCAAAAAATGGTGTTATACGTTGTACATGCTCTAAGCAATACGTTGTACATACTCT
AAGCAATA
Found at i:55362 original size:2 final size:2
Alignment explanation
Indices: 55321--55353 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55311 AATATAATTA
55321 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 A
55354 CTCATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55630 original size:17 final size:18
Alignment explanation
Indices: 55600--55634 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55590 GTTAAATTTG
*
55600 AATAGTTTTCAAGTTAAT
1 AATAGTTTTAAAGTTAAT
55618 AATA-TTTTAAAGTTAAT
1 AATAGTTTTAAAGTTAAT
55635 TGCTCAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (18 bp):
AATAGTTTTAAAGTTAAT
Found at i:57057 original size:30 final size:30
Alignment explanation
Indices: 57021--57091 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
57011 TCTGATTTTC
57021 TCCTGAATTGACACAA-T-CGATAACGTTATA
1 TCCTGAATTGACACAAGTAC--TAACGTTATA
* * *
57051 TCCTGAAATAACACAAGTACTAACGTTGTA
1 TCCTGAATTGACACAAGTACTAACGTTATA
57081 TCCTGAATTGA
1 TCCTGAATTGA
57092 ATTTCGCGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 32 0.94
31 1 0.03
32 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.30
Consensus pattern (30 bp):
TCCTGAATTGACACAAGTACTAACGTTATA
Done.