Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014742.1 Corchorus olitorius cultivar O-4 contig14775, 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: 60536
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2245 original size:21 final size:21
Alignment explanation
Indices: 2221--2287 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 21
2211 GTTTATCATC
2221 ATTTTATAGGTAATTAT-ACAA
1 ATTTTATAGGTAATTATCA-AA
* **
2242 ATTTCATATGGTGGTTATCAAA
1 ATTTTATA-GGTAATTATCAAA
*
2264 ATTTTATAGGGTGATTATCGAAA
1 ATTTTATA-GGTAATTATC-AAA
2287 A
1 A
2288 ATCATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 7 0.19
22 25 0.68
23 5 0.14
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.40
Consensus pattern (21 bp):
ATTTTATAGGTAATTATCAAA
Found at i:2259 original size:22 final size:22
Alignment explanation
Indices: 2240--2287 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2230 GTAATTATAC
* *
2240 AAATTTCATATGGTGGTTATCA
1 AAATTTCATAGGGTGATTATCA
*
2262 AAATTTTATAGGGTGATTATCGA
1 AAATTTCATAGGGTGATTATC-A
2285 AAA
1 AAA
2288 ATCATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (22 bp):
AAATTTCATAGGGTGATTATCA
Found at i:18089 original size:142 final size:142
Alignment explanation
Indices: 17833--18117 Score: 525
Period size: 142 Copynumber: 2.0 Consensus size: 142
17823 AAAAGGATTA
17833 TTCCAAAAGTCCTTATTATGGCAGTTAATGCAATAAGAATGGCAGGCAATTAAAGCAGATAGTTC
1 TTCCAAAAGTCCTTATTATGGCAGTTAATGCAATAAGAATGGCAGGCAATTAAAGCAGATAGTTC
*
17898 ATATGACAGGAAGCTTTAAAACATTATTATGGAAGAAAGAACATAAGTTCTCACAGTGTTGTAGT
66 ATATGACAGGAAGCTTTAAAACATTATTATGGAAGAAAGAACATAAGTTCTCACAGTGTTCTAGT
17963 CAATGCTCATAG
131 CAATGCTCATAG
17975 TTCCAAAAGTCCTTATTATGGCAGTTAATGCAATAAGAATGGCAGGCAATTAAAGCAGATAGTTC
1 TTCCAAAAGTCCTTATTATGGCAGTTAATGCAATAAGAATGGCAGGCAATTAAAGCAGATAGTTC
* * *
18040 ATATGACAGGAAGCTTTTAAACATTGTTATGGAAGAAAGAACATAAGTTCTCAGAGTGTTCTAGT
66 ATATGACAGGAAGCTTTAAAACATTATTATGGAAGAAAGAACATAAGTTCTCACAGTGTTCTAGT
*
18105 CAATGTTCATAG
131 CAATGCTCATAG
18117 T
1 T
18118 GAAGTAAGTT
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (142 bp):
TTCCAAAAGTCCTTATTATGGCAGTTAATGCAATAAGAATGGCAGGCAATTAAAGCAGATAGTTC
ATATGACAGGAAGCTTTAAAACATTATTATGGAAGAAAGAACATAAGTTCTCACAGTGTTCTAGT
CAATGCTCATAG
Found at i:26300 original size:69 final size:69
Alignment explanation
Indices: 26191--26350 Score: 284
Period size: 69 Copynumber: 2.3 Consensus size: 69
26181 TTTTGAACCA
*
26191 AGGCCAAGCACTACAGCCTATACTGACAATATCGGTCTTAAATCAATCGCGAATAAAGATTTCGA
1 AGGCCAAGCACTACAGCCTATACTGACAATATCGGCCTTAAATCAATCGCGAATAAAGATTTCGA
26256 GCCG
66 GCCG
* *
26260 AGGCCAAGCACTACAGCCTATACTGACGATGTCGGCCTTAAATCAATCGCGAATAAAGATTTCGA
1 AGGCCAAGCACTACAGCCTATACTGACAATATCGGCCTTAAATCAATCGCGAATAAAGATTTCGA
26325 GCCG
66 GCCG
*
26329 AGGCCAAGCACTACAGCATATA
1 AGGCCAAGCACTACAGCCTATA
26351 TAGAATGAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 87 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (69 bp):
AGGCCAAGCACTACAGCCTATACTGACAATATCGGCCTTAAATCAATCGCGAATAAAGATTTCGA
GCCG
Found at i:27243 original size:20 final size:20
Alignment explanation
Indices: 27218--27255 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27208 ATACTCCAAG
27218 TAATTATAGTAATATTTGAT
1 TAATTATAGTAATATTTGAT
*
27238 TAATTATAGTACTATTTG
1 TAATTATAGTAATATTTG
27256 GCATGGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50
Consensus pattern (20 bp):
TAATTATAGTAATATTTGAT
Found at i:29051 original size:78 final size:78
Alignment explanation
Indices: 28861--29028 Score: 246
Period size: 78 Copynumber: 2.2 Consensus size: 78
28851 TTCTCAAGAG
* * * * * *
28861 AAATCGTTTGTTAAGGATTTCGAACCCAGGCCTAACGTTTCGGCTTATGGTGGGGATGGTAATCT
1 AAATCATTTGCTAAAGATTTCGAACCCAGGCCCAACGTTTCGGCTTATGGTGAGAATGGTAATCT
*
28926 TAGAGGAGAGAAA
66 TAAAGGAGAGAAA
* * *
28939 AAATCATTTGCTAAAGATTTCGAACCCAGGCCCAACGTTTCTGCTTATGGTGATAATGGTGATCT
1 AAATCATTTGCTAAAGATTTCGAACCCAGGCCCAACGTTTCGGCTTATGGTGAGAATGGTAATCT
29004 TAAAGGAGAGAAA
66 TAAAGGAGAGAAA
29017 AAATCATTTGCT
1 AAATCATTTGCT
29029 GCTGACTTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (78 bp):
AAATCATTTGCTAAAGATTTCGAACCCAGGCCCAACGTTTCGGCTTATGGTGAGAATGGTAATCT
TAAAGGAGAGAAA
Found at i:31458 original size:25 final size:26
Alignment explanation
Indices: 31410--31464 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
31400 AGGATGGTAC
*
31410 AATACAAATTGAATTTTTCTAAATAA
1 AATAAAAATTGAATTTTTCTAAATAA
*
31436 AATAAAAATTGAA-TTTTGTAAATAA
1 AATAAAAATTGAATTTTTCTAAATAA
31461 AATA
1 AATA
31465 TTTTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (26 bp):
AATAAAAATTGAATTTTTCTAAATAA
Found at i:31643 original size:25 final size:27
Alignment explanation
Indices: 31591--31656 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
31581 AAAAGTACAC
*
31591 AAAATTATATTTTAATAGTGGCATAA-TT
1 AAAA-TATATTTTAATAATGGCA-AATTT
*
31619 AAAATATTTTTTAATAATGGC-AATTT
1 AAAATATATTTTAATAATGGCAAATTT
31645 AGAAATATATTT
1 A-AAATATATTT
31657 GGAGAAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 3 0.09
27 24 0.73
28 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGCAAATTT
Found at i:32846 original size:27 final size:25
Alignment explanation
Indices: 32797--32852 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 25
32787 TTTCCACTAT
32797 TTTAATAATGAAATAATTAAAATATTA
1 TTTAATAATGAAAT-ATTAAAATA-TA
32824 TTTAATAATGACAAT-TTAGAAATATA
1 TTTAATAATGA-AATATTA-AAATATA
32850 TTT
1 TTT
32853 GAAAATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.30
27 16 0.59
28 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (25 bp):
TTTAATAATGAAATATTAAAATATA
Found at i:32997 original size:22 final size:22
Alignment explanation
Indices: 32972--33053 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
32962 TTGAACATTT
32972 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* *
32994 TTATTAAATTTTGATAACCACC
1 TTATGAAATTTTGATAACTACC
* * *
33016 ATATGAAATTTTGGTAATTACC
1 TTATGAAATTTTGATAACTACC
* *
33038 -TATAAAATTGTGATAA
1 TTATGAAATTTTGATAA
33054 ACTCCATAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 13 0.26
22 37 0.74
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:33061 original size:43 final size:44
Alignment explanation
Indices: 32973--33076 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 44
32963 TGAACATTTT
* * *
32973 TATGAAATTTTGATAACTACCTTATTAAATTTTGATAACCACCA
1 TATGAAATTTTGATAACTACCTTATAAAATTGTGATAAACACCA
* * *
33017 TATGAAATTTTGGTAATTACC-TATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTACCTTATAAAATTGTGATAAACACCA
* **
33060 TAAGAAACCTTGATAAC
1 TATGAAATTTTGATAAC
33077 CTAACTATGA
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
43 30 0.61
44 19 0.39
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCTTATAAAATTGTGATAAACACCA
Found at i:35960 original size:16 final size:16
Alignment explanation
Indices: 35936--35970 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
35926 ATTCGTACTT
35936 TTATATATAGTATATAGA
1 TTATATATAG--TATAGA
35954 TTATATATAGTATAGA
1 TTATATATAGTATAGA
35970 T
1 T
35971 AGATAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (16 bp):
TTATATATAGTATAGA
Found at i:38767 original size:22 final size:22
Alignment explanation
Indices: 38725--38783 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
38715 AGGGAGGAAG
38725 AAAGAAGAGAAAAAAAAAAGAA
1 AAAGAAGAGAAAAAAAAAAGAA
* *
38747 AAAGAA-AGAACAAGAACAAGAA
1 AAAGAAGAGAA-AAAAAAAAGAA
*
38769 CAAGAAGA-AAAAAAA
1 AAAGAAGAGAAAAAAA
38784 GACAAGTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 8 0.26
22 22 0.71
23 1 0.03
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAGAAGAGAAAAAAAAAAGAA
Found at i:44066 original size:18 final size:18
Alignment explanation
Indices: 44035--44165 Score: 208
Period size: 18 Copynumber: 7.1 Consensus size: 18
44025 ATTATTATAC
44035 ATGTATGGTCAAACCCCAA
1 ATGT-TGGTCAAACCCCAA
*
44054 ATGTTGGTAAAACCCCAA
1 ATGTTGGTCAAACCCCAA
44072 ATGTTGGTCAAACCCCAA
1 ATGTTGGTCAAACCCCAA
*
44090 ATGTTGGTAAAACCCCAA
1 ATGTTGGTCAAACCCCAA
44108 ATGTATGGTCAAACCCCAA
1 ATGT-TGGTCAAACCCCAA
*
44127 ATGTTGGCCAAACCCCAA
1 ATGTTGGTCAAACCCCAA
44145 ATGTATGGTCAAACCCCAA
1 ATGT-TGGTCAAACCCCAA
44164 AT
1 AT
44166 TTCGGTAAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
18 68 0.65
19 36 0.35
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (18 bp):
ATGTTGGTCAAACCCCAA
Found at i:44126 original size:37 final size:37
Alignment explanation
Indices: 44035--44176 Score: 243
Period size: 37 Copynumber: 3.9 Consensus size: 37
44025 ATTATTATAC
44035 ATGTATGGTCAAACCCCAAATGTTGGTAAAACCCCAA
1 ATGTATGGTCAAACCCCAAATGTTGGTAAAACCCCAA
44072 ATGT-TGGTCAAACCCCAAATGTTGGTAAAACCCCAA
1 ATGTATGGTCAAACCCCAAATGTTGGTAAAACCCCAA
**
44108 ATGTATGGTCAAACCCCAAATGTTGGCCAAACCCCAA
1 ATGTATGGTCAAACCCCAAATGTTGGTAAAACCCCAA
44145 ATGTATGGTCAAACCCCAAAT-TTCGGTAAAAC
1 ATGTATGGTCAAACCCCAAATGTT-GGTAAAAC
44177 ACAAAATATT
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
36 38 0.38
37 61 0.62
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (37 bp):
ATGTATGGTCAAACCCCAAATGTTGGTAAAACCCCAA
Found at i:44514 original size:18 final size:18
Alignment explanation
Indices: 44491--44527 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
44481 TGTTTATGCA
44491 TGGTCAAACCCCAAATTT
1 TGGTCAAACCCCAAATTT
44509 TGGTCAAACCCCAAATTT
1 TGGTCAAACCCCAAATTT
44527 T
1 T
44528 AATAGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (18 bp):
TGGTCAAACCCCAAATTT
Found at i:44537 original size:21 final size:19
Alignment explanation
Indices: 44493--44560 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 19
44483 TTTATGCATG
*
44493 GTCAAACCCCAAATTT-TG
1 GTCAAACCCCAAATTTATA
44511 GTCAAACCCCAAATTTTAATA
1 GTCAAACCCCAAA-TTT-ATA
44532 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAA-TTT-ATA
*
44553 ATCAAACC
1 GTCAAACC
44561 ACATTAAACC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.30
19 3 0.07
21 27 0.63
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.25
Consensus pattern (19 bp):
GTCAAACCCCAAATTTATA
Found at i:44708 original size:14 final size:14
Alignment explanation
Indices: 44689--44715 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44679 ATTGATATTA
44689 AATATTAAAAAATT
1 AATATTAAAAAATT
44703 AATATTAAAAAAT
1 AATATTAAAAAAT
44716 AGAAACAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATTAAAAAATT
Found at i:46111 original size:15 final size:15
Alignment explanation
Indices: 46089--46132 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
46079 GGGAGGAAGT
46089 GGGAAGGAAAGAAGAG
1 GGGAAGGAAAGAA-AG
46105 GGG-AGGAAAGAAAG
1 GGGAAGGAAAGAAAG
*
46119 GGGAAGGAAGGAAA
1 GGGAAGGAAAGAAA
46133 AGACTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 18 0.69
16 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GGGAAGGAAAGAAAG
Found at i:49195 original size:15 final size:15
Alignment explanation
Indices: 49175--49212 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
49165 TTGGGGTTTG
49175 TATTTAGTTGCTGCA
1 TATTTAGTTGCTGCA
49190 TATTTAGTTGCTGCA
1 TATTTAGTTGCTGCA
49205 -ATTT-GTTG
1 TATTTAGTTG
49213 TAGTTCGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 15 0.65
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (15 bp):
TATTTAGTTGCTGCA
Found at i:49479 original size:27 final size:27
Alignment explanation
Indices: 49439--49503 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
49429 AGAAATCTAC
** *
49439 TTGATTTATTTTGGTTATATTTTGTAA
1 TTGATTTAGATTGGTCATATTTTGTAA
49466 TTGATTTAGATTGGTCATATTTTGTAA
1 TTGATTTAGATTGGTCATATTTTGTAA
49493 TTGATTTAGAT
1 TTGATTTAGAT
49504 GACATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.02, G:0.17, T:0.57
Consensus pattern (27 bp):
TTGATTTAGATTGGTCATATTTTGTAA
Found at i:50226 original size:16 final size:16
Alignment explanation
Indices: 50202--50254 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
50192 TATGACTTCC
* *
50202 TTTCTCTTCCTCCCTA
1 TTTCCCTTCCTTCCTA
*
50218 TTTCCCTTCCCTTGCTA
1 TTTCCCTT-CCTTCCTA
*
50235 TTTCCTTTCCTTCCTA
1 TTTCCCTTCCTTCCTA
50251 TTTC
1 TTTC
50255 TTTCCTCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.06, C:0.40, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTCCCTTCCTTCCTA
Found at i:55005 original size:2 final size:2
Alignment explanation
Indices: 54998--55035 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
54988 CAGTAGCAGA
54998 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
55036 TTCAAGGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57212 original size:21 final size:21
Alignment explanation
Indices: 56733--57211 Score: 622
Period size: 21 Copynumber: 22.8 Consensus size: 21
56723 TCTAATTTTA
* *
56733 GGGTTTGACTCTCAAAATTTG
1 GGGTTTGACTATCAAACTTTG
* *
56754 TGGTTTGACTATCAAACTTTA
1 GGGTTTGACTATCAAACTTTG
*
56775 GGGTTTGACTATCAAATTTTG
1 GGGTTTGACTATCAAACTTTG
*
56796 GGGTTTGACTACCAAACTTTG
1 GGGTTTGACTATCAAACTTTG
* *
56817 GGGTTTGACTATAAAATTTTG
1 GGGTTTGACTATCAAACTTTG
* *
56838 GGGTTTGACTTTCAAAATTTG
1 GGGTTTGACTATCAAACTTTG
*
56859 GGGTTTGACTATCAAATTTTG
1 GGGTTTGACTATCAAACTTTG
* *
56880 GGGTTTGACTTTCAAACTTTA
1 GGGTTTGACTATCAAACTTTG
**
56901 CAGTTTGACTATCAAACTTTG
1 GGGTTTGACTATCAAACTTTG
* *
56922 GGGTTTGACTATAAAATTTTG
1 GGGTTTGACTATCAAACTTTG
* * *
56943 GGGTTCGACTTTCAAAATTTG
1 GGGTTTGACTATCAAACTTTG
*
56964 GGGTTTGACTATCAAATTTTG
1 GGGTTTGACTATCAAACTTTG
* *
56985 GGGTTTGACTACCAAACTTTT
1 GGGTTTGACTATCAAACTTTG
*
57006 GGGTTTGACTACCAAACTTTG
1 GGGTTTGACTATCAAACTTTG
57027 GGGTTTGACTATCAAACTTTTAG
1 GGGTTTGACTATCAAAC-TTT-G
57050 GGG-TTGACTATCAAACTTTTG
1 GGGTTTGACTATCAAAC-TTTG
57071 GGGTTTGACTATCAAACTTTG
1 GGGTTTGACTATCAAACTTTG
57092 GGGTTTGACTATCAAACTTTG
1 GGGTTTGACTATCAAACTTTG
*
57113 GGATTTGACTATCAAACTTTG
1 GGGTTTGACTATCAAACTTTG
*
57134 GGTTTTGACTATCAAACTTT-
1 GGGTTTGACTATCAAACTTTG
* *
57154 GGGTTTGA-TAGTTAAAATTTG
1 GGGTTTGACTA-TCAAACTTTG
* *
57175 GGGTTTAACTATCAAAATTTG
1 GGGTTTGACTATCAAACTTTG
*
57196 GGGGTTGACTATCAAA
1 GGGTTTGACTATCAAA
57212 ACATCATTGT
Statistics
Matches: 403, Mismatches: 49, Indels: 12
0.87 0.11 0.03
Matches are distributed among these distances:
19 2 0.00
20 14 0.03
21 348 0.86
22 35 0.09
23 4 0.01
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (21 bp):
GGGTTTGACTATCAAACTTTG
Found at i:57312 original size:53 final size:53
Alignment explanation
Indices: 57249--57476 Score: 323
Period size: 53 Copynumber: 4.3 Consensus size: 53
57239 CCAAAGGATG
*
57249 ATGGTCAAACCTCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* * * * * * *
57302 ATGGTTAAACCCCAAAATTTAATATTCGAATCATATAACATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* *
57355 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC-AATCACCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* *
57407 ATAGTCAAACCCCAAAATTCAATAGTCAAACCACAAAATATCATTGTACATGC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* *
57460 ATAGTTAAACCCCAAAA
1 ATGGTCAAACCCCAAAA
57477 GATGATGTTC
Statistics
Matches: 152, Mismatches: 22, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
52 48 0.32
53 104 0.68
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (53 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
Found at i:57453 original size:105 final size:106
Alignment explanation
Indices: 57249--57476 Score: 323
Period size: 105 Copynumber: 2.2 Consensus size: 106
57239 CCAAAGGATG
* * * *
57249 ATGGTCAAACCTCAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTTAAACCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCC
* * * * * *
57314 CAAAATTTAATATTCGAATCATATAACATCATTGTACATGC
66 CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
*
57355 ATGGTCAAACCCCAAAATTCAATAGTCAAACCAC-AATCACCATTGTACATGCATAGTCAAACCC
1 ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCC
*
57419 CAAAATTCAATAGTCAAACCACAAAATATCATTGTACATGC
66 CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
* *
57460 ATAGTTAAACCCCAAAA
1 ATGGTCAAACCCCAAAA
57477 GATGATGTTC
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
105 75 0.69
106 33 0.31
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (106 bp):
ATGGTCAAACCCCAAAATTCAATAGTCAAACCACAAAACACCATTGTACATGCATAGTCAAACCC
CAAAATTCAATAGTCAAACCACAAAACATCATTGTACATGC
Found at i:58118 original size:28 final size:28
Alignment explanation
Indices: 58087--58153 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
58077 TAAGAGAGTT
*
58087 AACAAGACATTTTTTTTGGCCAAATAAA
1 AACAAGACATTTTTTTTGGCCAAACAAA
58115 AACAAGACATTTTTTTTGGCCAAACAAA
1 AACAAGACATTTTTTTTGGCCAAACAAA
58143 AACAAGACATT
1 AACAAGACATT
58154 ATTTCACCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (28 bp):
AACAAGACATTTTTTTTGGCCAAACAAA
Found at i:59345 original size:18 final size:19
Alignment explanation
Indices: 59322--59358 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
59312 TTGTTACCTT
59322 AATTATG-TTTTTTTTAGA
1 AATTATGATTTTTTTTAGA
59340 AATTATGATTTTTTTTAGA
1 AATTATGATTTTTTTTAGA
59359 GGTACATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (19 bp):
AATTATGATTTTTTTTAGA
Done.