Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012329.1 Corchorus olitorius cultivar O-4 contig12362, 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: 88349
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5221 original size:19 final size:18
Alignment explanation
Indices: 5188--5223 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5178 TTGAGATAAT
5188 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
5206 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
5224 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:6985 original size:15 final size:16
Alignment explanation
Indices: 6943--6985 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
6933 TTTATTTACA
*
6943 TTAGT-TTAG-TTTAG
1 TTAGTCTTAGTTTTTG
6957 TTAGTCTTAGTTTTTG
1 TTAGTCTTAGTTTTTG
6973 TTA-TCTTAGTTTT
1 TTAGTCTTAGTTTT
6986 CCTGCACTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 14 0.54
16 7 0.27
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.63
Consensus pattern (16 bp):
TTAGTCTTAGTTTTTG
Found at i:9233 original size:38 final size:38
Alignment explanation
Indices: 9145--9483 Score: 318
Period size: 38 Copynumber: 8.9 Consensus size: 38
9135 TCAAAGTTAG
* * * * ** * *
9145 CTGGAAACAGGTAATCTTTCAGAAGTTACCGATGTTGG
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
*
9183 CTGAAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
* * * * * * *
9221 ATGGAAAGAGGTCATCTTTCAGCAATTAACGAAGTTGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
* *
9259 CTGGAAATAGGTCATCTTTCAACAGTTATCAAAATCGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
* * * * *
9297 CTGGAAACAGTTCTTCTTTCAGCTGTTATCCAAGTCGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
* * * *
9335 CTGGAAACATGTTATCTTTTAGCAGTTGTCAAAATCGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
*
9373 CTGGAAACAGGTCATCTTTCAGCAGTTATCGAAATCGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
** * * * *
9411 GGGGAGACAGGTCATCTTTCAGCTGTTGTCAAAGTCGA
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
* * * ***
9449 CTAGAAAGAGGTCCTCTTTCAATTGTTATCAAAAT
1 CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAAT
9484 TGACCCAGTT
Statistics
Matches: 238, Mismatches: 63, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
38 238 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (38 bp):
CTGGAAACAGGTCATCTTTCAGCAGTTATCAAAATCGA
Found at i:10407 original size:64 final size:64
Alignment explanation
Indices: 10293--10418 Score: 198
Period size: 64 Copynumber: 2.0 Consensus size: 64
10283 ACAAATTGAT
* * * *
10293 TCAAGATGTTCTTTTCTTCTCCTATATTGTTGCTGCATTGCGCAAGGTAGCTCACATAAGCTAA
1 TCAAGATGTTCTTTTCTTCTCCTATAATGTTGCTGCATTGCCCAACGTAGCTCACAAAAGCTAA
* *
10357 TCAATATGTTCTTTTCTTCTCCTATAATGTTGTTGCATTGCCCAACGTAGCTCACAAAAGCT
1 TCAAGATGTTCTTTTCTTCTCCTATAATGTTGCTGCATTGCCCAACGTAGCTCACAAAAGCT
10419 TTTCCTGGAG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (64 bp):
TCAAGATGTTCTTTTCTTCTCCTATAATGTTGCTGCATTGCCCAACGTAGCTCACAAAAGCTAA
Found at i:23156 original size:38 final size:38
Alignment explanation
Indices: 23110--23216 Score: 144
Period size: 38 Copynumber: 2.8 Consensus size: 38
23100 ATGTCTTTAA
23110 TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
1 TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
* * *
23148 TTAGGTAATTCCGAAAGAAAATTTTGGGAAAAATAAAAGT
1 TTAAGTAATTCCAAAAGAAGATTTT-GG-AAAATAAAAGT
* *
23188 TTAAG-AAATCCAAAAGAAGTTTTTGGAAA
1 TTAAGTAATTCCAAAAGAAGATTTTGGAAA
23217 TTAATAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
37 3 0.05
38 24 0.41
39 17 0.29
40 15 0.25
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (38 bp):
TTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGT
Found at i:26477 original size:16 final size:16
Alignment explanation
Indices: 26456--26491 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
26446 TCATTTCTCT
*
26456 CCACACACCCGTACAC
1 CCACACACCCATACAC
*
26472 CCACACACCCATATAC
1 CCACACACCCATACAC
26488 CCAC
1 CCAC
26492 TGAATACACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.56, G:0.03, T:0.08
Consensus pattern (16 bp):
CCACACACCCATACAC
Found at i:33208 original size:26 final size:25
Alignment explanation
Indices: 33179--33250 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
33169 GTTCGAAGAA
33179 ATTGATCGGAAGACGGTCCTCGAAAG
1 ATTGATCGGAAGACGGTCCTCG-AAG
* *
33205 ATTGAAT-TGAAGACAGT--TCGAAG
1 ATTG-ATCGGAAGACGGTCCTCGAAG
33228 ATGTTGATCGGAAGACGGTCCTC
1 A--TTGATCGGAAGACGGTCCTC
33251 TTAAGAATGG
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
23 4 0.11
24 5 0.14
25 11 0.31
26 12 0.33
27 4 0.11
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.24
Consensus pattern (25 bp):
ATTGATCGGAAGACGGTCCTCGAAG
Found at i:33241 original size:25 final size:24
Alignment explanation
Indices: 33161--33353 Score: 72
Period size: 25 Copynumber: 7.5 Consensus size: 24
33151 AGTTTGAATT
*
33161 GGAAGACAGTTCGAAGAAATTGATC
1 GGAAGACAGTTCGAAG-AGTTGATC
*
33186 GGAAGACGGTCCTCGAA-AGATTGAAT-
1 GGAAGACAGT--TCGAAGAG-TTG-ATC
*
33212 TGAAGACAGTTCGAAGATGTTGATC
1 GGAAGACAGTTCGAAGA-GTTGATC
* * * * *
33237 GGAAGACGGTCCTCTTAAGAATGGAATT
1 GGAAGACAGT--TC-GAAGAGTTG-ATC
* *
33265 GGAAGACAATTCGAAGAAGTTGATTT
1 GGAAGACAGTTCGAAG-AGTTGA-TC
* *
33291 GGAAGAC-GATCCTCCAA-AGATTGAATT
1 GGAAGACAG-T--TCGAAGAG-TTG-ATC
33318 GGAAGACAGTTCGAAGAAGTTGATC
1 GGAAGACAGTTCGAAG-AGTTGATC
*
33343 GGGAGAC-GTTC
1 GGAAGACAGTTC
33354 CACTCAGAAG
Statistics
Matches: 127, Mismatches: 20, Indels: 43
0.67 0.11 0.23
Matches are distributed among these distances:
24 11 0.09
25 38 0.30
26 32 0.25
27 26 0.20
28 20 0.16
ACGTcount: A:0.35, C:0.13, G:0.29, T:0.23
Consensus pattern (24 bp):
GGAAGACAGTTCGAAGAGTTGATC
Found at i:33287 original size:53 final size:52
Alignment explanation
Indices: 33068--33350 Score: 324
Period size: 53 Copynumber: 5.5 Consensus size: 52
33058 TTCATAAAAG
* *
33068 AGTTCG-A-AAGTTGATCGGAAGACGATCCTTTTAAGATTGAATTGGAAGAC
1 AGTTCGAAGAAGTTGATCGGAAGACGGTCCTCTTAAGATTGAATTGGAAGAC
* * * * * * * *
33118 AGTTC-AA-AGGATAAGCGAAAGACGGTTCTTTTAAGTTTGAATTGGAAGAC
1 AGTTCGAAGAAGTTGATCGGAAGACGGTCCTCTTAAGATTGAATTGGAAGAC
* **
33168 AGTTCGAAGAAATTGATCGGAAGACGGTCCTCGAAAGATTGAATT-GAAGAC
1 AGTTCGAAGAAGTTGATCGGAAGACGGTCCTCTTAAGATTGAATTGGAAGAC
* *
33219 AGTTCGAAGATGTTGATCGGAAGACGGTCCTCTTAAGAATGGAATTGGAAGAC
1 AGTTCGAAGAAGTTGATCGGAAGACGGTCCTCTTAAG-ATTGAATTGGAAGAC
* * * **
33272 AATTCGAAGAAGTTGATTTGGAAGACGATCCTCCAAAGATTGAATTGGAAGAC
1 AGTTCGAAGAAGTTGA-TCGGAAGACGGTCCTCTTAAGATTGAATTGGAAGAC
*
33325 AGTTCGAAGAAGTTGATCGGGAGACG
1 AGTTCGAAGAAGTTGATCGGAAGACG
33351 TTCCACTCAG
Statistics
Matches: 193, Mismatches: 34, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
50 46 0.24
51 41 0.21
52 40 0.21
53 49 0.25
54 17 0.09
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (52 bp):
AGTTCGAAGAAGTTGATCGGAAGACGGTCCTCTTAAGATTGAATTGGAAGAC
Found at i:33295 original size:26 final size:26
Alignment explanation
Indices: 33263--33341 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
33253 AAGAATGGAA
33263 TTGGAAGACAATTCGAAGAAGTTGAT
1 TTGGAAGACAATTCGAAGAAGTTGAT
* * *
33289 TTGGAAGACGATCCTC-CA-AAGATTGAA
1 TTGGAAGACAAT--TCGAAGAAG-TTGAT
*
33316 TTGGAAGACAGTTCGAAGAAGTTGAT
1 TTGGAAGACAATTCGAAGAAGTTGAT
33342 CGGGAGACGT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
25 2 0.05
26 19 0.46
27 18 0.44
28 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (26 bp):
TTGGAAGACAATTCGAAGAAGTTGAT
Found at i:34011 original size:22 final size:22
Alignment explanation
Indices: 33970--34012 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33960 TTGTTGTTAT
* **
33970 AAAAGTAAAAAAATTTTAAAAA
1 AAAAGGAAAAAAATCATAAAAA
33992 AAAAGGAAAAAAATCATAAAA
1 AAAAGGAAAAAAATCATAAAA
34013 TCACAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAAGGAAAAAAATCATAAAAA
Found at i:37393 original size:16 final size:15
Alignment explanation
Indices: 37372--37402 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
37362 AGGATTTCAT
37372 TTCTTTAAGTTATTTG
1 TTCTTTAAGTT-TTTG
37388 TTCTTTAAGTTTTTG
1 TTCTTTAAGTTTTTG
37403 GCTTAATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.16, C:0.06, G:0.13, T:0.65
Consensus pattern (15 bp):
TTCTTTAAGTTTTTG
Found at i:37986 original size:38 final size:38
Alignment explanation
Indices: 37935--38035 Score: 143
Period size: 38 Copynumber: 2.7 Consensus size: 38
37925 TTTTAATTGA
* *
37935 GTAATTGC-AAAGAAGATTTTGGAAAATATAAGTTTAG
1 GTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTAG
*
37972 GTAATTCCAAAAGAAGATTTTGGAATAATAAAAGTTTAT
1 GTAATTCCAAAAGAAGATTTTGGAA-AATAAAAGTTTAG
*
38011 G-AAATCCAAAAGAAGATTTTGGAAA
1 GTAATTCCAAAAGAAGATTTTGGAAA
38036 CTAATAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
37 8 0.14
38 38 0.66
39 12 0.21
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (38 bp):
GTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTAG
Found at i:38709 original size:11 final size:11
Alignment explanation
Indices: 38693--38723 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
38683 CTTGTTTTTT
38693 GTTTTTGTTTC
1 GTTTTTGTTTC
*
38704 GTTTTTGTTTT
1 GTTTTTGTTTC
38715 GTTTTTGTT
1 GTTTTTGTT
38724 ACCCTGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.19, T:0.77
Consensus pattern (11 bp):
GTTTTTGTTTC
Found at i:41746 original size:36 final size:36
Alignment explanation
Indices: 41696--41764 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
41686 TTAACAATAG
**
41696 GCAATATAGGCTTGTTTCTAGTGGATGGATACTGAA
1 GCAATATACACTTGTTTCTAGTGGATGGATACTGAA
* *
41732 GCAATATACACTTGTTTCTATTGGATGGGTACT
1 GCAATATACACTTGTTTCTAGTGGATGGATACT
41765 TCAAGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (36 bp):
GCAATATACACTTGTTTCTAGTGGATGGATACTGAA
Found at i:55660 original size:6 final size:6
Alignment explanation
Indices: 55649--55674 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55639 TAATCAGTAA
55649 AATGGT AATGGT AATGGT AATGGT AA
1 AATGGT AATGGT AATGGT AATGGT AA
55675 AGAGTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (6 bp):
AATGGT
Found at i:55742 original size:35 final size:36
Alignment explanation
Indices: 55661--55768 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 36
55651 TGGTAATGGT
*
55661 AATGGTAATGGTAAAGAGTAAAAAAGTAATAAGTCA
1 AATGGTAATGGTAAAGAGTAAAAAAGTAATAAGTAA
* **
55697 AATGGTAATGGTAAAGAGTAAAGAA-TAATCTGTAA
1 AATGGTAATGGTAAAGAGTAAAAAAGTAATAAGTAA
*
55732 AATGGTAATGGTAAAGAGT-AAAAAGTAATTAGTAA
1 AATGGTAATGGTAAAGAGTAAAAAAGTAATAAGTAA
55767 AA
1 AA
55769 GAGTAATAGC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
34 4 0.06
35 36 0.56
36 24 0.38
ACGTcount: A:0.52, C:0.02, G:0.22, T:0.24
Consensus pattern (36 bp):
AATGGTAATGGTAAAGAGTAAAAAAGTAATAAGTAA
Found at i:55769 original size:22 final size:22
Alignment explanation
Indices: 55744--55924 Score: 135
Period size: 22 Copynumber: 8.4 Consensus size: 22
55734 TGGTAATGGT
*
55744 AAAGAGTAAAAAGTAATTAGTA
1 AAAGAGTAAAAAGTAATCAGTA
* * *
55766 AAAGAGT-AATAGCAATCGGT-
1 AAAGAGTAAAAAGTAATCAGTA
*
55786 AAAGAGTAAAGAGTAATCA--A
1 AAAGAGTAAAAAGTAATCAGTA
* *
55806 AAA-ATGTTAATAGTAATCAGT-
1 AAAGA-GTAAAAAGTAATCAGTA
* * **
55827 AAAGAG-AAAAGAATAATTAAAAAA
1 AAAGAGTAAAA-AGTAA-T-CAGTA
* *
55851 AAAGGGT-AATAGTAATCAGTA
1 AAAGAGTAAAAAGTAATCAGTA
*
55872 AAAGAGTAAAAAGTAATCAATA
1 AAAGAGTAAAAAGTAATCAGTA
55894 AAAGAGTAAAAAGTAATCAGTA
1 AAAGAGTAAAAAGTAATCAGTA
*
55916 TAAGAGTAA
1 AAAGAGTAA
55925 TTTCAATCAG
Statistics
Matches: 121, Mismatches: 26, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
19 1 0.01
20 24 0.20
21 33 0.27
22 51 0.42
23 5 0.04
24 7 0.06
ACGTcount: A:0.57, C:0.04, G:0.18, T:0.20
Consensus pattern (22 bp):
AAAGAGTAAAAAGTAATCAGTA
Found at i:55787 original size:83 final size:83
Alignment explanation
Indices: 55623--55801 Score: 211
Period size: 83 Copynumber: 2.1 Consensus size: 83
55613 AAAAAAAAAG
* * * **
55623 GGTAAAAAGTAAAGAGTAATCAGTAAAATGGTAATGGTAATGGTAATGGTAAAGAGTAAAAAAGT
1 GGTAAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAAAGGTAAAAGTAAAGAGTAAAAAAGT
*
55688 AATAAGTCAAATGGTAAT
66 AATAAGTCAAATGGTAAA
* ** *
55706 GGTAAAGAGTAAAGAATAATCTGTAAAATGGTAATGGTAAAGAGTAAAAAGTAATTAGTAAAAGA
1 GGTAAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAAAG-GT-AAAAGTAAAGAGTAAAAAA
55771 GTAAT-AG-C-AATCGGTAAA
64 GTAATAAGTCAAAT-GGTAAA
55789 GAGTAAAGAGTAA
1 G-GTAAAGAGTAA
55802 TCAAAAAATG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
82 3 0.04
83 45 0.55
84 15 0.18
85 19 0.23
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.23
Consensus pattern (83 bp):
GGTAAAGAGTAAAGAATAATCAGTAAAATGGTAATGGTAAAGGTAAAAGTAAAGAGTAAAAAAGT
AATAAGTCAAATGGTAAA
Found at i:55909 original size:44 final size:42
Alignment explanation
Indices: 55742--55924 Score: 183
Period size: 44 Copynumber: 4.3 Consensus size: 42
55732 AATGGTAATG
* * * *
55742 GTAAAGAGTAAAAAGTAATTAGTAAAAGAGTAATAGCAATCG
1 GTAAAGAGTAAAAAGTAATCAATAAAAGAGTAATAGTAATCA
* *
55784 GTAAAGAGTAAAGAGTAATCAA-AAAATG-TTAATAGTAATCA
1 GTAAAGAGTAAAAAGTAATCAATAAAA-GAGTAATAGTAATCA
* * * *
55825 GTAAAGAG-AAAAGAATAATTAAAAAAAAAGGGTAATAGTAATCA
1 GTAAAGAGTAAAA-AGTAA-T-CAATAAAAGAGTAATAGTAATCA
*
55869 GTAAAAGAGTAAAAAGTAATCAATAAAAGAGTAAAAAGTAATCA
1 GT-AAAGAGTAAAAAGTAATCAATAAAAGAGT-AATAGTAATCA
55913 GTATAAGAGTAA
1 GTA-AAGAGTAA
55925 TTTCAATCAG
Statistics
Matches: 116, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
40 3 0.03
41 26 0.22
42 21 0.18
43 13 0.11
44 39 0.34
45 10 0.09
46 4 0.03
ACGTcount: A:0.57, C:0.04, G:0.19, T:0.21
Consensus pattern (42 bp):
GTAAAGAGTAAAAAGTAATCAATAAAAGAGTAATAGTAATCA
Found at i:56468 original size:35 final size:36
Alignment explanation
Indices: 56365--56468 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 36
56355 ATTTTAGGTC
*
56365 TTTTCAAATTGGGAAGGTTCCCATCCAGTTTTCAGAG
1 TTTTCAAATTGGGAAAGTTCCCAT-CAGTTTTCAGAG
*
56402 TTTTCAAATTGGGAAAGTTCCCATGAGTTTTCA-AG
1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAGAG
*
56437 TTTTCAAATTGGGAAAAGTTCCTATCA-TTTTC
1 TTTTCAAATTGGG-AAAGTTCCCATCAGTTTTC
56469 GGTTTTAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
35 20 0.32
36 19 0.31
37 23 0.37
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (36 bp):
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAGAG
Found at i:59154 original size:19 final size:19
Alignment explanation
Indices: 59130--59169 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59120 CTAAAGTTAA
*
59130 AATGCCTAAATGCAAGCCC
1 AATGCCCAAATGCAAGCCC
*
59149 AATGCCCAAGTGCAAGCCC
1 AATGCCCAAATGCAAGCCC
59168 AA
1 AA
59170 AGCTATGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (19 bp):
AATGCCCAAATGCAAGCCC
Found at i:60058 original size:12 final size:13
Alignment explanation
Indices: 60028--60069 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
60018 TCATGCACCC
*
60028 AAAACAATTTATTT
1 AAAACAATTTA-AT
*
60042 AAAACCATTT-AT
1 AAAACAATTTAAT
60054 AAAACAATTTAAT
1 AAAACAATTTAAT
60067 AAA
1 AAA
60070 TCAGTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 5 0.21
14 9 0.38
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAACAATTTAAT
Found at i:60960 original size:19 final size:19
Alignment explanation
Indices: 60938--60980 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
60928 TTTTCCTTCC
*
60938 CTTTTTCTTTTCTTTC-TTT
1 CTTTTTC-TTCCTTTCTTTT
60957 CTTTTTCTTCCTTTCTTTT
1 CTTTTTCTTCCTTTCTTTT
60976 CTTTT
1 CTTTT
60981 CTTATTGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
CTTTTTCTTCCTTTCTTTT
Found at i:60961 original size:18 final size:19
Alignment explanation
Indices: 60940--60983 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
60930 TTCCTTCCCT
*
60940 TTTTCTTTTCTTTC-TTTC
1 TTTTCTTTCCTTTCTTTTC
60958 TTTT-TCTTCCTTTCTTTTC
1 TTTTCT-TTCCTTTCTTTTC
60977 TTTTCTT
1 TTTTCTT
60984 ATTGGGCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 9 0.41
20 1 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCCTTTCTTTTC
Found at i:60962 original size:14 final size:13
Alignment explanation
Indices: 60941--60979 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
60931 TCCTTCCCTT
60941 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
*
60954 TTTCTTTTTCTTCC
1 TTTC-TTTTCTTTC
60968 TTTCTTTTCTTT
1 TTTCTTTTCTTT
60980 TCTTATTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:61687 original size:2 final size:2
Alignment explanation
Indices: 61676--61704 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
61666 TCCTTGTAAT
61676 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61705 ATTCATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:61952 original size:11 final size:10
Alignment explanation
Indices: 61907--61952 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
61897 GAAATAATTT
*
61907 TTCAATGATC
1 TTCAATTATC
61917 TTC-A-TATC
1 TTCAATTATC
61925 TTCAAATTATC
1 TTC-AATTATC
61936 TTCAATTAATC
1 TTCAATT-ATC
61947 TTCAAT
1 TTCAAT
61953 CACGAACTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 8 0.26
11 16 0.52
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.46
Consensus pattern (10 bp):
TTCAATTATC
Found at i:65127 original size:6 final size:7
Alignment explanation
Indices: 65114--65154 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
65104 TAACTTTAAG
65114 ATTAAAA
1 ATTAAAA
65121 ATTAAAA
1 ATTAAAA
65128 ATTAAAAA
1 ATT-AAAA
*
65136 AATAAGAA
1 ATTAA-AA
65144 ATTAAAA
1 ATTAAAA
65151 ATTA
1 ATTA
65155 TTGGGTTGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 18 0.60
8 12 0.40
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
ATTAAAA
Found at i:65138 original size:16 final size:16
Alignment explanation
Indices: 65117--65151 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
65107 CTTTAAGATT
*
65117 AAAAATTAA-AAATTA
1 AAAAAATAAGAAATTA
65132 AAAAAATAAGAAATTA
1 AAAAAATAAGAAATTA
65148 AAAA
1 AAAA
65152 TTATTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAAAATAAGAAATTA
Found at i:66870 original size:21 final size:21
Alignment explanation
Indices: 66846--66886 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
66836 TTGGAGCTCA
66846 TTGAATTCAAAATTAGGGTTC
1 TTGAATTCAAAATTAGGGTTC
*
66867 TTGAGTTCAAAATTAGGGTT
1 TTGAATTCAAAATTAGGGTT
66887 TTTGGTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGAATTCAAAATTAGGGTTC
Found at i:74029 original size:27 final size:28
Alignment explanation
Indices: 73956--74032 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
73946 TTAGGATCAA
*
73956 CTAGGGGCATTTTGGTCATTCTCAAGAAT
1 CTAGGGGCATTTTGGTCATT-TCAACAAT
* *
73985 CTAGGGGCATTTTAGTCATTTGC-ACATT
1 CTAGGGGCATTTTGGTCATTT-CAACAAT
74013 C-AGGGGCATTTTGGTCATTT
1 CTAGGGGCATTTTGGTCATTT
74033 TAAGTTCACA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 18 0.42
28 5 0.12
29 20 0.47
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTCAACAAT
Found at i:74327 original size:26 final size:26
Alignment explanation
Indices: 74295--74370 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 26
74285 TTTTTTCTTT
*
74295 CACATTAGTAATTAGGTAATAACATC
1 CACATTAGTAATTAGGCAATAACATC
* * * *
74321 CATATTAGTAATTAGGCATTAGCATT
1 CACATTAGTAATTAGGCAATAACATC
*
74347 CACATTAGTAATTAGGCATTAACA
1 CACATTAGTAATTAGGCAATAACA
74371 GTTTGCGATC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (26 bp):
CACATTAGTAATTAGGCAATAACATC
Found at i:75214 original size:17 final size:17
Alignment explanation
Indices: 75192--75268 Score: 136
Period size: 17 Copynumber: 4.5 Consensus size: 17
75182 GCTCTCTGAA
75192 TCACCTCTCAAACACTC
1 TCACCTCTCAAACACTC
75209 TCACCTCTCAAACACTC
1 TCACCTCTCAAACACTC
*
75226 TCACATCTCAAACACTC
1 TCACCTCTCAAACACTC
75243 TCACCTCTCAAACACTC
1 TCACCTCTCAAACACTC
*
75260 TCATCTCTC
1 TCACCTCTC
75269 CCATTCAAGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.29, C:0.45, G:0.00, T:0.26
Consensus pattern (17 bp):
TCACCTCTCAAACACTC
Found at i:83948 original size:46 final size:46
Alignment explanation
Indices: 83898--84006 Score: 184
Period size: 46 Copynumber: 2.4 Consensus size: 46
83888 TTAGATAAAG
*
83898 CTCTTGATCCAGTGTGAATTATCCTTTTTATACTTTAAACAAATT-C
1 CTCTTGATCCAGTGTGAATTATCCCTTTTATACTTTAAAC-AATTAC
*
83944 CTCTTGATCCAGTGTGAATTATCCCTTTTATTCTTTAAACAATTAC
1 CTCTTGATCCAGTGTGAATTATCCCTTTTATACTTTAAACAATTAC
83990 CTCTTGATCCAGTGTGA
1 CTCTTGATCCAGTGTGA
84007 TAATTACTCA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
45 4 0.07
46 56 0.93
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (46 bp):
CTCTTGATCCAGTGTGAATTATCCCTTTTATACTTTAAACAATTAC
Found at i:86268 original size:27 final size:27
Alignment explanation
Indices: 86238--86310 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
86228 AGGATCAACT
86238 AGGGGCATTTCGGTCATTTGCACATTC
1 AGGGGCATTTCGGTCATTTGCACATTC
* **
86265 AGGGGTATTTTAGTCATTTGCACATTC
1 AGGGGCATTTCGGTCATTTGCACATTC
86292 AGGGGCA-TTCTGGTCATTT
1 AGGGGCATTTC-GGTCATTT
86311 TAAGTTCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (27 bp):
AGGGGCATTTCGGTCATTTGCACATTC
Done.