Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014939.1 Corchorus olitorius cultivar O-4 contig14972, 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: 174122
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:804 original size:45 final size:45
Alignment explanation
Indices: 748--893 Score: 274
Period size: 45 Copynumber: 3.2 Consensus size: 45
738 AAGTTAGAAT
*
748 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
793 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
*
838 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
883 CCATGATTGCC
1 CCATGATTGCC
894 GAGTGCACAA
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (45 bp):
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC
Found at i:5376 original size:22 final size:23
Alignment explanation
Indices: 5351--5396 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5341 AAACATATGC
* *
5351 AAAAA-CTAATAATATCACTTTA
1 AAAAATCTAAAAAAATCACTTTA
*
5373 AAAAATCTAAAAAAATCATTTTA
1 AAAAATCTAAAAAAATCACTTTA
5396 A
1 A
5397 TAATATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAATCTAAAAAAATCACTTTA
Found at i:7792 original size:2 final size:2
Alignment explanation
Indices: 7785--7809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7775 CGGAGCGAAG
7785 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
7810 CTTGTTTGGG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:18613 original size:14 final size:14
Alignment explanation
Indices: 18594--18632 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
18584 GGGGATATTT
18594 AGGTGTATTTTGTA
1 AGGTGTATTTTGTA
18608 AGGTGTATTTTGTA
1 AGGTGTATTTTGTA
18622 AGGTGTATTTT
1 AGGTGTATTTT
18633 TTACTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
AGGTGTATTTTGTA
Found at i:56569 original size:74 final size:76
Alignment explanation
Indices: 56424--56575 Score: 290
Period size: 75 Copynumber: 2.0 Consensus size: 76
56414 GATCATGTTT
56424 ATAGAATATTAATAAGCAAAACTAAAAAAGAAATATTAAGAAAGATAAAAAGAAAGAATGGTGAA
1 ATAGAATATTAATAAGCAAAACTAAAAAAGAAATATTAAGAAAGATAAAAAGAAAGAATGGTGAA
56489 GGACTAATTGC
66 GGACTAATTGC
56500 ATAGAAT-TTAATAAGCAAAACTAAAAAAGAAATATTAAGAAAGAT-AAAAGAAAGAATGGTGAA
1 ATAGAATATTAATAAGCAAAACTAAAAAAGAAATATTAAGAAAGATAAAAAGAAAGAATGGTGAA
56563 GGACTAATTGC
66 GGACTAATTGC
56574 AT
1 AT
56576 GAAATCAAAT
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 31 0.41
75 38 0.50
76 7 0.09
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.20
Consensus pattern (76 bp):
ATAGAATATTAATAAGCAAAACTAAAAAAGAAATATTAAGAAAGATAAAAAGAAAGAATGGTGAA
GGACTAATTGC
Found at i:68718 original size:36 final size:36
Alignment explanation
Indices: 68678--68749 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
68668 TGAAACCTGG
68678 AAGAAAGCGCAACATGAAGCCCTCTGATGCCAATGT
1 AAGAAAGCGCAACATGAAGCCCTCTGATGCCAATGT
68714 AAGAAAGCGCAACATGAAGCCCTCTGATGCCAATGT
1 AAGAAAGCGCAACATGAAGCCCTCTGATGCCAATGT
68750 GCTGAATGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (36 bp):
AAGAAAGCGCAACATGAAGCCCTCTGATGCCAATGT
Found at i:70279 original size:247 final size:250
Alignment explanation
Indices: 69347--70335 Score: 1602
Period size: 255 Copynumber: 3.9 Consensus size: 250
69337 AGATTCTTGA
* *
69347 AGAAATTGAAAGGACAATAGATGCAACAGGTCTTCGTGGAAAAA-TCGAGGAGTTAAAGGAAGAG
1 AGAAATTGAAAGGACAATAGATGCAGCAGGTCTTCGT-GAAAAATTCGAGGAGTTTAAGGAAGAG
* * *
69411 TTGGCT-GTAGGCTCTACTTCATCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGTAATTC
65 TTGGCTCG-AGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGGAATTC
69475 TTGCTGCCTTGAATAACAACGCATCACTAAAAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCA
129 TTGCTGCCTTGAATAACAAC-CAT-AC---AAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCA
*
69540 TCATTCCAGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGACGAAGAGATTATTGG
189 TCATTCCAGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGACGAAGAGATTAGTGG
*
69602 AGTAATTGAAAGGACAATAGATGCAGCAGGTCTTCGTGAAAAATTCGAGGAGTTTAAGGAAGAGT
1 AGAAATTGAAAGGACAATAGATGCAGCAGGTCTTCGTGAAAAATTCGAGGAGTTTAAGGAAGAGT
*
69667 TGGCTCAAGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGGAATTCTT
66 TGGCTCGAGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGGAATTCTT
69732 GCTGCCTTGAATAACAACGCATCACTAAAAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCATC
131 GCTGCCTTGAATAACAAC-CAT-AC---AAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCATC
*
69797 ATTCCAGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGATGAAGAGATTAGTGG
191 ATTCCAGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGACGAAGAGATTAGTGG
* * *
69857 AGAAATTGAAATGACAATAGATGCAGCAGGTCTTCATGAAAAATTTGAGGAGTTTAAGGAAGAGT
1 AGAAATTGAAAGGACAATAGATGCAGCAGGTCTTCGTGAAAAATTCGAGGAGTTTAAGGAAGAGT
*
69922 TGGCTCGAGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCATGGAGGGAATTCTT
66 TGGCTCGAGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGGAATTCTT
69987 GCTGCCTTGAATAAC-A-CAT-C-AGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCATCATTCC
131 GCTGCCTTGAATAACAACCATACAAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCATCATTCC
70048 AGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGACGAAGAGATTAGTGG
196 AGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGACGAAGAGATTAGTGG
*
70103 AGAAATTGAAGGGACAATAGATGCAGCAGGTCTTCGTGGAAAAATTCGAGGAGTTTAAGGAAGAG
1 AGAAATTGAAAGGACAATAGATGCAGCAGGTCTTCGT-GAAAAATTCGAGGAGTTTAAGGAAGAG
* *
70168 TTGGCTCGAGACTCTACTTCACCAAAAGTACAAAAATTGGAAACTGAGATCAAGGAGGGGATTCT
65 TTGGCTCGAGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGGAATTCT
*
70233 TGCTGCCTTGAATAAC-A-CAT-C-AGAGAGGGTTGAGAATCTAAGAGCAGAGCTTTCATCATTC
130 TGCTGCCTTGAATAACAACCATACAAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCATCATTC
* ** *
70294 CAGGAAATAGCCACTGATGATGAGGTTTTTCTTCCTGCTGAC
195 CAGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGAC
70336 AATGGCAGAT
Statistics
Matches: 703, Mismatches: 28, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
246 129 0.18
247 186 0.26
250 1 0.00
252 3 0.00
254 7 0.01
255 377 0.54
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (250 bp):
AGAAATTGAAAGGACAATAGATGCAGCAGGTCTTCGTGAAAAATTCGAGGAGTTTAAGGAAGAGT
TGGCTCGAGACTCTACTTCACCAAAAGTACAAAAACTGGAAACTGAGATCAAGGAGGGAATTCTT
GCTGCCTTGAATAACAACCATACAAGAGAAGGTTGAGAATCTAAGAGCAGAGCTTTCATCATTCC
AGGAAATAGCCACCGATGATGAGGTTTCACTTACTGCTGACGAAGAGATTAGTGG
Found at i:70953 original size:3 final size:3
Alignment explanation
Indices: 70939--70981 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
70929 CACAAACTTG
70939 ATA ATA ATTA ATA ATA ATA ATA ATA AT- ATA ATGCA ATA ATA AT
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT--A ATA ATA AT
70982 TTCCAAAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 3 0.08
5 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:70960 original size:16 final size:18
Alignment explanation
Indices: 70939--70982 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
70929 CACAAACTTG
70939 ATAATAATTA-ATAAT-A
1 ATAATAATTATATAATCA
*
70955 ATAATAATAATATAATGCA
1 ATAATAATTATATAAT-CA
70974 ATAATAATT
1 ATAATAATT
70983 TCCAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
19 9 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAATAATTATATAATCA
Found at i:70963 original size:19 final size:21
Alignment explanation
Indices: 70939--70981 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
70929 CACAAACTTG
70939 ATAATAAT-TAAT-AATAATA
1 ATAATAATATAATCAATAATA
70958 ATAATAATATAATGCAATAATA
1 ATAATAATATAAT-CAATAATA
70980 AT
1 AT
70982 TTCCAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
22 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAATAATATAATCAATAATA
Found at i:72158 original size:21 final size:21
Alignment explanation
Indices: 72132--72178 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
72122 TCACCAGCAA
* * *
72132 CAACAACAGCATCATCACCAG
1 CAACAACAGCAGCAGCAACAG
72153 CAACAACAGCAGCAGCAACAG
1 CAACAACAGCAGCAGCAACAG
72174 CAACA
1 CAACA
72179 GCAGTGGCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.36, G:0.13, T:0.04
Consensus pattern (21 bp):
CAACAACAGCAGCAGCAACAG
Found at i:72173 original size:12 final size:12
Alignment explanation
Indices: 72126--72175 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
72116 GCAGTTTCAC
*
72126 CAGCAACAACAA
1 CAGCAACAACAG
* * *
72138 CAGCATCATCAC
1 CAGCAACAACAG
72150 CAGCAACAACAG
1 CAGCAACAACAG
*
72162 CAGCAGCAACAG
1 CAGCAACAACAG
72174 CA
1 CA
72176 ACAGCAGTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.46, C:0.36, G:0.14, T:0.04
Consensus pattern (12 bp):
CAGCAACAACAG
Found at i:83988 original size:48 final size:51
Alignment explanation
Indices: 83923--84017 Score: 142
Period size: 48 Copynumber: 1.9 Consensus size: 51
83913 TTTAGTATAA
83923 TAGATTCATTTAATTAAAGAGTC-CG-GATTACAAACACC-GGGATAGTAG
1 TAGATTCATTTAATTAAAGAGTCTCGAGATTACAAACACCAGGGATAGTAG
* * *
83971 TAGATTTATTTAATTAAAGAGTCTGGAGATTTCAAACACCAGGGATA
1 TAGATTCATTTAATTAAAGAGTCTCGAGATTACAAACACCAGGGATA
84018 AAGTCGGTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
48 22 0.54
49 1 0.02
50 12 0.29
51 6 0.15
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (51 bp):
TAGATTCATTTAATTAAAGAGTCTCGAGATTACAAACACCAGGGATAGTAG
Found at i:84537 original size:112 final size:113
Alignment explanation
Indices: 84336--84558 Score: 342
Period size: 112 Copynumber: 2.0 Consensus size: 113
84326 TATCCTAAAA
* * **
84336 AAACAAATTAAAATTGGCTTATTACTTGAATGAATTGCTAGGGATTAAAAAAGAAAGGAAGGAAT
1 AAACAAATTAAAATTGGCTTATTACTTGAATGAATTACTAAGGAAAAAAAAAGAAAGGAAGGAAT
*
84401 AAGAGTTTACTTACTGTTAATAGCAAAC-AAAAATCAGAATCTCATAT
66 AAGAGTTTACTTACTGATAATAGCAAACAAAAAATCAGAATCTCATAT
*
84448 AAACAAATTAAAATTGGGTTATTACTTGAATGAATTACTAAGGAAAAAAAAAGGAAAGGAAGGAA
1 AAACAAATTAAAATTGGCTTATTACTTGAATGAATTACTAAGGAAAAAAAAA-GAAAGGAAGGAA
* **
84513 TAGGAGTTTACTTACT-ATGGTAGCAAACAAAAAATCAGAATCTCAT
65 TAAGAGTTTACTTACTGATAATAGCAAACAAAAAATCAGAATCTCAT
84559 GTCAAATTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
112 56 0.56
113 44 0.44
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (113 bp):
AAACAAATTAAAATTGGCTTATTACTTGAATGAATTACTAAGGAAAAAAAAAGAAAGGAAGGAAT
AAGAGTTTACTTACTGATAATAGCAAACAAAAAATCAGAATCTCATAT
Found at i:98942 original size:21 final size:21
Alignment explanation
Indices: 98918--98961 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
98908 TGATTGGTCC
98918 TTTTGAGTT-GAGGCCCAATAA
1 TTTTG-GTTCGAGGCCCAATAA
* *
98939 TTTTGTTTCTAGGCCCAATAA
1 TTTTGGTTCGAGGCCCAATAA
98960 TT
1 TT
98962 AATATTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (21 bp):
TTTTGGTTCGAGGCCCAATAA
Found at i:99448 original size:2 final size:2
Alignment explanation
Indices: 99441--99471 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
99431 TTCTAGTTAC
99441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99472 TAAGCTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:105995 original size:24 final size:25
Alignment explanation
Indices: 105963--106018 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
105953 AAAATATTAT
105963 TAATTTTTT-G-CTCTTATTGCTTGA
1 TAATTTTTTAGAC-CTTATTGCTTGA
105987 TAATTTTTTTAGAACCTTATTGCTTGA
1 TAA-TTTTTTAG-ACCTTATTGCTTGA
106014 TAATT
1 TAATT
106019 GATTGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 3 0.11
25 6 0.21
26 3 0.11
27 15 0.54
28 1 0.04
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (25 bp):
TAATTTTTTAGACCTTATTGCTTGA
Found at i:110200 original size:21 final size:21
Alignment explanation
Indices: 110176--110242 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
110166 AATTCTCTGT
110176 AAATTAAGAAATACTCAACTG
1 AAATTAAGAAATACTCAACTG
* * **
110197 AAATCATAGAAA-ATTC-TTTG
1 AAATTA-AGAAATACTCAACTG
*
110217 TAAATTAAGAAATACTCAACTC
1 -AAATTAAGAAATACTCAACTG
110239 AAAT
1 AAAT
110243 CCCGATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 7 0.21
21 20 0.61
22 6 0.18
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTG
Found at i:110222 original size:42 final size:42
Alignment explanation
Indices: 110163--110243 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
110153 GCTAAGTCTT
*
110163 GAAAATTCTCTGTAAATTAAGAAATACTCAACTGAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
110205 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
110244 CCGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:110387 original size:56 final size:56
Alignment explanation
Indices: 110309--110422 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
110299 TTTATTTTGT
*
110309 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTTTTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
**
110365 AGAATAATTAAGTAGAGTTAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
110421 AG
1 AG
110423 GAAACAGATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAAATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:113083 original size:43 final size:43
Alignment explanation
Indices: 113036--113139 Score: 172
Period size: 43 Copynumber: 2.4 Consensus size: 43
113026 AGTGAAGGAC
* *
113036 GATTCGAATCTGATTTTAATAAGTAGAATTTAGGTAAAGGAAA
1 GATTCGAATCCGATTTTAATAAGTAAAATTTAGGTAAAGGAAA
113079 GATTCGAATCCGATTTTAATAAGTAAAATTTAGGTAAAGGAAA
1 GATTCGAATCCGATTTTAATAAGTAAAATTTAGGTAAAGGAAA
* *
113122 GATTCAAACCCGATTTTA
1 GATTCGAATCCGATTTTA
113140 CAGTAAGATC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (43 bp):
GATTCGAATCCGATTTTAATAAGTAAAATTTAGGTAAAGGAAA
Found at i:113490 original size:43 final size:42
Alignment explanation
Indices: 113429--113531 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 42
113419 ATTAGAATTT
*
113429 TTCGAACCCAATTTTAATAAG-TCGAATTTAGGTAAAGGAAAGA
1 TTCGAA-CCAATTTTAAT-AGTTCGAATTTAGATAAAGGAAAGA
*
113472 TTCGAATCCAATTTTAATAGTTCGAATTTAGATAAAGGAAGGA
1 TTCGAA-CCAATTTTAATAGTTCGAATTTAGATAAAGGAAAGA
113515 TTCGAACCTAATTTTAA
1 TTCGAACC-AATTTTAA
113532 AGTGACATCT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
42 4 0.07
43 51 0.93
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (42 bp):
TTCGAACCAATTTTAATAGTTCGAATTTAGATAAAGGAAAGA
Found at i:113751 original size:43 final size:43
Alignment explanation
Indices: 113690--113795 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
113680 AAGATGAATG
*** * *
113690 AAAGATTCGAATTTGATTTTAATAAGTAGAATTTACATTAAA-A
1 AAAGATTCGAACCCGATTTTAATAAGTAAAATTTA-AGTAAAGA
*
113733 AAAGATTCGAACCCGATTTTAATAAGTAAAATTTAGGTAAAGA
1 AAAGATTCGAACCCGATTTTAATAAGTAAAATTTAAGTAAAGA
* *
113776 AAAGATGCGAGCCCGATTTT
1 AAAGATTCGAACCCGATTTT
113796 TAAAGTGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 4 0.07
43 50 0.93
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.31
Consensus pattern (43 bp):
AAAGATTCGAACCCGATTTTAATAAGTAAAATTTAAGTAAAGA
Found at i:114110 original size:2 final size:2
Alignment explanation
Indices: 114103--114141 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
114093 AAGAAATTGT
114103 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
114142 GTACACATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128287 original size:12 final size:12
Alignment explanation
Indices: 128270--128295 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
128260 CTACTCCTTA
128270 TTAAGCATAAGC
1 TTAAGCATAAGC
128282 TTAAGCATAAGC
1 TTAAGCATAAGC
128294 TT
1 TT
128296 GCCAGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (12 bp):
TTAAGCATAAGC
Found at i:140202 original size:10 final size:11
Alignment explanation
Indices: 140176--140203 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
140166 TCGAAACGAT
140176 GAAAAAAGAAA
1 GAAAAAAGAAA
140187 GAAAAAAGAAA
1 GAAAAAAGAAA
140198 GAAAAA
1 GAAAAA
140204 CGATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:140406 original size:8 final size:8
Alignment explanation
Indices: 140393--140443 Score: 102
Period size: 8 Copynumber: 6.4 Consensus size: 8
140383 CTAATTATAA
140393 GGATTTAT
1 GGATTTAT
140401 GGATTTAT
1 GGATTTAT
140409 GGATTTAT
1 GGATTTAT
140417 GGATTTAT
1 GGATTTAT
140425 GGATTTAT
1 GGATTTAT
140433 GGATTTAT
1 GGATTTAT
140441 GGA
1 GGA
140444 GGGATGCTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 43 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.47
Consensus pattern (8 bp):
GGATTTAT
Found at i:144830 original size:10 final size:10
Alignment explanation
Indices: 144815--144874 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
144805 TAGGGCAGAG
144815 CTTTCTCTTT
1 CTTTCTCTTT
144825 CTTTCTC-TT
1 CTTTCTCTTT
144834 CTCTTCTTCTTCTT
1 CT-TTC-TC-T-TT
*
144848 CTTCCTC-TT
1 CTTTCTCTTT
*
144857 CTTTCTCTCT
1 CTTTCTCTTT
144867 CTTTCTCT
1 CTTTCTCT
144875 ACAATAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
9 12 0.29
10 19 0.46
11 2 0.05
12 2 0.05
13 2 0.05
14 4 0.10
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (10 bp):
CTTTCTCTTT
Found at i:144849 original size:23 final size:20
Alignment explanation
Indices: 144815--144874 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 20
144805 TAGGGCAGAG
144815 CTTTCTCT-TTCTTTCTCTT
1 CTTTCTCTCTTCTTTCTCTT
*
144834 CTCTTCTTCTTCTTCTTCCTCTT
1 CT-TTC-TC-TCTTCTTTCTCTT
144857 CTTTCTCTC-TCTTTCTCT
1 CTTTCTCTCTTCTTTCTCT
144875 ACAATAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 10 0.29
20 5 0.14
21 4 0.11
22 4 0.11
23 12 0.34
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (20 bp):
CTTTCTCTCTTCTTTCTCTT
Found at i:146783 original size:16 final size:17
Alignment explanation
Indices: 146750--146782 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
146740 GATTTCTATA
146750 TATTAGTAGTATTGTTT
1 TATTAGTAGTATTGTTT
146767 TATTA-TAGTATT-TTT
1 TATTAGTAGTATTGTTT
146782 T
1 T
146783 TGTATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (17 bp):
TATTAGTAGTATTGTTT
Found at i:149629 original size:92 final size:92
Alignment explanation
Indices: 149472--149656 Score: 343
Period size: 92 Copynumber: 2.0 Consensus size: 92
149462 GAAAATGCTT
*
149472 GCTTCTCCCTATCAATTTGTTCATTAGTCATATGCCATAACCCTCTGTAGAAGCATTACCGGATG
1 GCTTCTCCCTATCAATTTGTTCATTAGTCATATGCCATAACCCTCCGTAGAAGCATTACCGGATG
*
149537 TCTGGACTCATCCTACCACACTAAGCC
66 TCTGGACTCAACCTACCACACTAAGCC
*
149564 GCTTCTCCCTATCAATTTGTTCATTAGTCATATGCCATAACCCTCCGTAGAAGCATTGCCGGATG
1 GCTTCTCCCTATCAATTTGTTCATTAGTCATATGCCATAACCCTCCGTAGAAGCATTACCGGATG
149629 TCTGGACTCAACCTACCACACTAAGCC
66 TCTGGACTCAACCTACCACACTAAGCC
149656 G
1 G
149657 GACATAACCA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (92 bp):
GCTTCTCCCTATCAATTTGTTCATTAGTCATATGCCATAACCCTCCGTAGAAGCATTACCGGATG
TCTGGACTCAACCTACCACACTAAGCC
Found at i:154450 original size:4 final size:4
Alignment explanation
Indices: 154441--154490 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
154431 GGAAAAAAGT
154441 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
154489 GA
1 GA
154491 CAGCAGTTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:155949 original size:24 final size:24
Alignment explanation
Indices: 155903--155950 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
155893 AAGCTTTTTT
*
155903 TTTTCCAAAAAGAGTAGATATAAG
1 TTTTCCAAAAAGAGTAGAAATAAG
155927 TTTTCCAAAAAGA-TAAGAAATAAG
1 TTTTCCAAAAAGAGT-AGAAATAAG
155951 GAGAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (24 bp):
TTTTCCAAAAAGAGTAGAAATAAG
Found at i:173267 original size:284 final size:284
Alignment explanation
Indices: 172755--173316 Score: 838
Period size: 284 Copynumber: 2.0 Consensus size: 284
172745 AATTCAGAAA
* * * * *
172755 CTCGTAAAAACAAATTCTTACATCCAATGTAGCTGACATTTGGTTCGATGAATACAGATATTTCA
1 CTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAACATTTGGTTAGATGAATACAGACATTTCA
* * *
172820 AGGAATCTTTGCGCCAAATATCATGCAAAATTGAGCTGGGGCTCCGGAACGCGTTTTTAGCCAAA
66 AGGAATCTTTGCGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAA
* * *
172885 AACCGTGATGGTTAATACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAGTTTTTCC
131 AACCGTAATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCC
* *
172950 TCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCTAAAAAATTAAAATGGTTTT
196 TCAAATTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATGGTTTT
173015 TCACGCTTCCAATATCGTCGGATG
261 TCACGCTTCCAATATCGTCGGATG
* * * *
173039 CTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGACATTTCA
1 CTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAACATTTGGTTAGATGAATACAGACATTTCA
* * * * * *
173104 ATGAGTTTTTGCGCCAAAAATCAAG-ATAAATTGAGCCGGGGCTGCTGAACTCGTTTTTAGCCAA
66 AGGAATCTTTGCGCCAAAAATCAAGCA-AAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAA
* * * *
173168 AAACTGTAATGGTTAATATACGATTTCATCTAAAATTTTGCAAAAACTTACCCGAAAAGTTTTTC
130 AAACCGTAATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTC
* * *
173233 CTCAAATTTTTGCCACAATACTCAGAAGAACTATATTCTTCAACCCCCAAAAATTAAAATGGTTT
195 CTCAAATTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATGGTTT
173298 TTCACGCTTCCAATATCGT
260 TTCACGCTTCCAATATCGT
173317 TCTTCCAATA
Statistics
Matches: 247, Mismatches: 30, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
283 1 0.00
284 246 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (284 bp):
CTCGTAAAAACAAATCCTTAAATCCAATGTAGCTAACATTTGGTTAGATGAATACAGACATTTCA
AGGAATCTTTGCGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAA
AACCGTAATGGTTAATACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCC
TCAAATTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATGGTTTT
TCACGCTTCCAATATCGTCGGATG
Found at i:173323 original size:14 final size:14
Alignment explanation
Indices: 173304--173331 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
173294 GTTTTTCACG
173304 CTTCCAATATCGTT
1 CTTCCAATATCGTT
173318 CTTCCAATATCGTT
1 CTTCCAATATCGTT
173332 TTTTTTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (14 bp):
CTTCCAATATCGTT
Found at i:173778 original size:328 final size:332
Alignment explanation
Indices: 173035--173984 Score: 1478
Period size: 328 Copynumber: 2.8 Consensus size: 332
173025 AATATCGTCG
*
173035 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGACAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATAT
* * * * *
173100 TTCAATGAGTTTTTGCGCCAAAAATCAAG-ATAAATTGAGCCGGGGCTGCTGAACTCGTTTTTAG
66 TTCAAGGAGTCTTTGCGCCAAAAATCAAGCA-AAATTGAGCCGGGGCTCCGGAACGCGTTTTTAG
* * * ** *
173164 CCAAAAACTGTAATGGTTAATATACGATTTCATCTAAAATTTTGCAAAAACTTACCCGAAAAGTT
130 CCAAAAACAGTGATGG-TAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTT
* * * *
173229 TTTCCTCAAATTTTTGCCACAATACTCAGAAGAACTATATTCTTCAACCCCCAAAAATTAAAATG
194 TTTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATG
173294 GTTTTTCACGCTTCCAATATCGTTCTTCCAATATCGTTTTTTTTTTCGAATTTATTTTTAATTAA
259 GTTTTTCACGCTTCCAATATCGTTCTTCC-A-A-----TTTTTTTTCGAATTTATTTTTAATTAA
173359 ATCGAAACAAGATTCA
317 ATCGAAACAAGATTCA
173375 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATAT
173440 TTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGC
66 TTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGC
* *
173505 CAAAAACAGTGAT-G-CATACACGATTTCGGCTAAATTTTTGCAAAAACTGACCCGAAAAGTTTT
131 CAAAAACAGTGATGGTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTT
*
173568 TCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAATTGGT
196 TCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATGGT
*
173633 TTTTCACGCTTCCAATATCGTTTTTCC-A-TTTTTTTCGAATTTATTTTTAATTAAATCGAAACA
261 TTTTCACGCTTCCAATATCGTTCTTCCAATTTTTTTTCGAATTTATTTTTAATTAAATCGAAACA
173696 AGATTCA
326 AGATTCA
*
173703 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAAATTTGGTTAGATGAATATAGATAT
1 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATAT
* * *
173768 TTCAAGGAGTCTTTGAGCCAACAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGC
66 TTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGC
* * * * *
173833 AAAAAACCGTGATGGTTAATACACGATTTTGGCTAAAATTTTACAAAAACTGACCCAAAAAGTTT
131 CAAAAACAGTGATGG-TAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTT
* * * *
173898 TTCCTCAATTCTTTGCCACAATACTCAGAAAAAATATATTATTCAACCCCGAAAAATTAAAATAG
195 TTCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATGG
173963 TTTTTCACGCTTCCAATATCGT
260 TTTTTCACGCTTCCAATATCGT
173985 CGGATGCTCA
Statistics
Matches: 570, Mismatches: 36, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
328 179 0.31
329 1 0.00
331 125 0.22
334 1 0.00
337 129 0.23
339 1 0.00
340 133 0.23
341 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (332 bp):
GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTAAGATTTGGTTAGATGAATATAGATAT
TTCAAGGAGTCTTTGCGCCAAAAATCAAGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGC
CAAAAACAGTGATGGTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTT
TCCTCAATTTTTTGCCACAATACTCAGAAAAACTATATTATTCAACCCCAAAAAATTAAAATGGT
TTTTCACGCTTCCAATATCGTTCTTCCAATTTTTTTTCGAATTTATTTTTAATTAAATCGAAACA
AGATTCA
Done.