Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015066.1 Corchorus capsularis cultivar CVL-1 contig15087, 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: 38394
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3182 original size:15 final size:15
Alignment explanation
Indices: 3162--3194 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3152 CCTCTCTAGC
3162 CATAGAGGGGTGCGA
1 CATAGAGGGGTGCGA
3177 CATAGAGGGGTGCGA
1 CATAGAGGGGTGCGA
3192 CAT
1 CAT
3195 CCCTAGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.15, G:0.42, T:0.15
Consensus pattern (15 bp):
CATAGAGGGGTGCGA
Found at i:6246 original size:69 final size:69
Alignment explanation
Indices: 6124--6258 Score: 182
Period size: 69 Copynumber: 2.0 Consensus size: 69
6114 AAACTAACAG
*** * * * *
6124 CTAAGGAAAAAATGGTGGGAACACCATTAATTACATCTCAATGTTATACTTACATATAAAGACAA
1 CTAAGGAAAAAATGACAGGAACACCATGAATTACATCTCAATGCTAAAATTACATATAAAGACAA
6189 TACA
66 TACA
*
6193 CTAAGGAAAAAATGACAGGAACACCATGAATTGCATC-CAAATGCTAAAATTACATATAAAGACA
1 CTAAGGAAAAAATGACAGGAACACCATGAATTACATCTC-AATGCTAAAATTACATATAAAGACA
6257 AT
65 AT
6259 GCATTTCAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 1 0.02
69 56 0.98
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.23
Consensus pattern (69 bp):
CTAAGGAAAAAATGACAGGAACACCATGAATTACATCTCAATGCTAAAATTACATATAAAGACAA
TACA
Found at i:6474 original size:22 final size:22
Alignment explanation
Indices: 6449--6491 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6439 ATTAGTATAT
* *
6449 TATTTTTGGAGGGGCCATTGAC
1 TATTTTTGAAGGAGCCATTGAC
6471 TATTTTTGAAGGAGCCATTGA
1 TATTTTTGAAGGAGCCATTGA
6492 TTGGTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (22 bp):
TATTTTTGAAGGAGCCATTGAC
Found at i:6704 original size:31 final size:29
Alignment explanation
Indices: 6666--6774 Score: 121
Period size: 31 Copynumber: 3.6 Consensus size: 29
6656 TTAAAAGGCT
*
6666 AAATGCTCAATTTGGTACCAAACCTTTCA
1 AAATGCTCAATTTGATACCAAACCTTTCA
* *
6695 TGAAATGCTCAATTTTATACTAAACC-TTCA
1 --AAATGCTCAATTTGATACCAAACCTTTCA
* *
6725 AAGTTGCTCAAATTGATACCAAACCTTTCA
1 AA-ATGCTCAATTTGATACCAAACCTTTCA
6755 AAATCAGCTCAATTTGATAC
1 AAAT--GCTCAATTTGATAC
6775 TTTTTCAACA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.03
29 19 0.29
30 10 0.15
31 34 0.52
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (29 bp):
AAATGCTCAATTTGATACCAAACCTTTCA
Found at i:8710 original size:31 final size:29
Alignment explanation
Indices: 8674--8775 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 29
8664 TCTTAAAATA
*
8674 GTATCAAATTGAGCTTA-TTTAAAAATGTTTG
1 GTATCAAATTGAG-ATAGTTT-AAAA-GTTTG
* *
8705 GTATCAATTTGAGATAGTTTTAAAGTTTG
1 GTATCAAATTGAGATAGTTTAAAAGTTTG
* ** *
8734 GTATGAAATTGAGATTTTCTTGAAAGGTTTG
1 GTATCAAATTGAGATAGT-TT-AAAAGTTTG
*
8765 GTACCAAATTG
1 GTATCAAATTG
8776 GGATTTTAGC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 19 0.33
30 7 0.12
31 31 0.54
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (29 bp):
GTATCAAATTGAGATAGTTTAAAAGTTTG
Found at i:9852 original size:86 final size:86
Alignment explanation
Indices: 9694--9853 Score: 214
Period size: 86 Copynumber: 1.8 Consensus size: 86
9684 TTCTTGGCTA
* * * * *
9694 AACAATGAGGAGAGGAAGAGGAACGATGGAGAAGAAAGACTTTGTAGAAGTTGGTTTAGTGAAAT
1 AACAATGAGAAGAGGAAGAGGAACGAAGAAGAAGAAAGACTTTGTAAAAGTTGGTTTAGTGAAAA
9759 AAAAAAAAGTAAATTACGTTG
66 AAAAAAAAGTAAATTACGTTG
* * * *
9780 AACAATGTGAAGAGGATGAGGAAGGAAGAAGAAGAAAGACTTT-TAAAAGTTGGTTTAGTATAAA
1 AACAATGAGAAGAGGAAGAGGAACGAAGAAGAAGAAAGACTTTGTAAAAGTTGGTTTAGT-GAAA
9844 AAAGAAAAAA
65 AAA-AAAAAA
9854 TTACCCTGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
85 15 0.24
86 42 0.67
87 6 0.10
ACGTcount: A:0.49, C:0.04, G:0.28, T:0.20
Consensus pattern (86 bp):
AACAATGAGAAGAGGAAGAGGAACGAAGAAGAAGAAAGACTTTGTAAAAGTTGGTTTAGTGAAAA
AAAAAAAAGTAAATTACGTTG
Found at i:13855 original size:37 final size:37
Alignment explanation
Indices: 13717--13942 Score: 314
Period size: 37 Copynumber: 6.1 Consensus size: 37
13707 AGAACAGTAA
*
13717 AAAGTACTTAATTCAGGGTAATTAAGTAAAGAGCAGTTT
1 AAAGGACTTAATTCAGGGTAATTAAGTAAA-AGCAG-TT
*
13756 AAAGAACTTAATTCAGGGTAATTAAGTAAAAG--GTT
1 AAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* * *
13791 -AAGAACTTAATTCAGGGCAATTTAGTAAAAGCAGTT
1 AAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* *
13827 AAAGGACTTAATTCTGGGTAATTAAGTAAAAGTAGTT
1 AAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
* * *
13864 GAAGGACTTAATTTAGGGAAATTAAGTAAAAGCAGTT
1 AAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
*
13901 GAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
1 AAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
13938 AAAGG
1 AAAGG
13943 GTAAGGATAA
Statistics
Matches: 168, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
34 29 0.17
35 2 0.01
36 4 0.02
37 102 0.61
38 2 0.01
39 29 0.17
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.28
Consensus pattern (37 bp):
AAAGGACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
Found at i:13992 original size:41 final size:41
Alignment explanation
Indices: 13942--14200 Score: 256
Period size: 41 Copynumber: 6.6 Consensus size: 41
13932 GCAGTTAAAG
*
13942 GGTAAGGATAAACACAGACTTAATTTCAAGGAAGGAAATTA
1 GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
*
13983 GGTAAGGATAAGCACAGACTTAATTTTAAGGAAGGAAATTA
1 GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
** * *
14024 GGTAAGGACGAGCATAGACTTAA-TTC-AGG-A--TAATTA
1 GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
* * * *
14060 AGTAAAG-TAAGCACAGACTTAATTCCAAGGAAGCAAATTA
1 GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
* *
14100 GGTAAGGACAAGCACAGACTTAA-TTC-A-G--GGTAATTA
1 GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
* * * *
14136 AGTAAAG-TAATCACACACTTAATTTCAAGGAAGGAAATTA
1 GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
* *
14176 GGTAAAG-TCAAACACAGACTTAATT
1 GGTAAGGAT-AAGCACAGACTTAATT
14201 CGGGGTAATT
Statistics
Matches: 177, Mismatches: 29, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
35 24 0.14
36 26 0.15
37 4 0.02
38 4 0.02
39 4 0.02
40 28 0.16
41 87 0.49
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (41 bp):
GGTAAGGATAAGCACAGACTTAATTTCAAGGAAGGAAATTA
Found at i:14078 original size:35 final size:35
Alignment explanation
Indices: 14034--14252 Score: 143
Period size: 35 Copynumber: 5.9 Consensus size: 35
14024 GGTAAGGACG
*
14034 AGCATAGACTTAATTCAGGATAATTAAGTAAAGTA
1 AGCACAGACTTAATTCAGGATAATTAAGTAAAGTA
* * * *
14069 AGCACAGACTTAATTCCAAGGAAGCAAATTAGGTAAGGACA
1 AGCACAGACTTAATT-C-AGG-A--TAATTAAGTAAAG-TA
*
14110 AGCACAGACTTAATTCAGGGTAATTAAGTAAAGTA
1 AGCACAGACTTAATTCAGGATAATTAAGTAAAGTA
* * * *
14145 ATCACACACTTAATTTCAAGGAAGGAAATTAGGTAAAGTCA
1 AGCACAGACTTAA-TTC-AGG-A--TAATTAAGTAAAGT-A
* * * * *
14186 AACACAGACTTAATTCGGGGTAATTAGGTAAA-TT
1 AGCACAGACTTAATTCAGGATAATTAAGTAAAGTA
* ** *
14220 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
1 AGCACAGACTTAA-TTCAGGATAATTAAGTAAA
14253 ATCATTAAAG
Statistics
Matches: 142, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
34 11 0.08
35 40 0.28
36 25 0.18
37 6 0.04
38 1 0.01
39 5 0.04
40 26 0.18
41 28 0.20
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (35 bp):
AGCACAGACTTAATTCAGGATAATTAAGTAAAGTA
Found at i:14091 original size:76 final size:76
Alignment explanation
Indices: 13974--14237 Score: 343
Period size: 76 Copynumber: 3.5 Consensus size: 76
13964 ATTTCAAGGA
* * * *
13974 AGGA-AATTAGGTAAGGATAAGCACAGACTTAATTTTAAGGAAGGAAATTAGGTAAGGACGAGCA
1 AGGATAATTAAGTAAAG-TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAGGACAAGCA
*
14038 TAGACTTAATTC
65 CAGACTTAATTC
* *
14050 AGGATAATTAAGTAAAGTAAGCACAGACTTAATTCCAAGGAAGCAAATTAGGTAAGGACAAGCAC
1 AGGATAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAGGACAAGCAC
14115 AGACTTAATTC
66 AGACTTAATTC
* * * * * *
14126 AGGGTAATTAAGTAAAGTAATCACACACTTAATTTCAAGGAAGGAAATTAGGTAAAGTCAAACAC
1 AGGATAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAGGACAAGCAC
14191 AGACTTAATTC
66 AGACTTAATTC
* * * * *
14202 GGGGTAATTAGGTAAA-TTAGCAAAGACTTAATTTCA
1 AGGATAATTAAGTAAAGTAAGCACAGACTTAATTTCA
14238 CAAGAATTAA
Statistics
Matches: 166, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
75 16 0.10
76 140 0.84
77 10 0.06
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (76 bp):
AGGATAATTAAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAGGACAAGCAC
AGACTTAATTC
Found at i:14192 original size:117 final size:114
Alignment explanation
Indices: 13950--14201 Score: 269
Period size: 117 Copynumber: 2.2 Consensus size: 114
13940 AGGGTAAGGA
* * *
13950 TAAACACAGACTTAATTTCAAGGAAGGAAATTAGGTAAGGATAAGCACAGACTTAATTTTAAGGA
1 TAAACACAGACTTAATTCCAAGGAAGCAAATTAGGTAAGGACAAGCACAGACTTAA-TTTAAGG-
* * * *
14015 AGGAAATTAGGTAAGGACGAGCATAGACTTAATTCAGGATAATTAAGTAAAG
64 AGGAAATTAAGTAAGGAC-AGCACACACTTAATTCAGGAAAATTAAGTAAAG
* *
14067 TAAGCACAGACTTAATTCCAAGGAAGCAAATTAGGTAAGGACAAGCACAGACTTAA-TTCA-G-G
1 TAAACACAGACTTAATTCCAAGGAAGCAAATTAGGTAAGGACAAGCACAGACTTAATTTAAGGAG
* * * *
14129 GTAATTAAGTAAAGTA-ATCACACACTTAATTTCAAGGAAGGAAATTAGGTAAAG
66 GAAATTAAGT-AAGGACAGCACACACTTAA-TTC-AGG-A--AAATTAAGTAAAG
14183 TCAAACACAGACTTAATTC
1 T-AAACACAGACTTAATTC
14202 GGGGTAATTA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
111 10 0.09
112 12 0.11
113 7 0.06
114 2 0.02
115 3 0.03
116 12 0.11
117 68 0.60
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (114 bp):
TAAACACAGACTTAATTCCAAGGAAGCAAATTAGGTAAGGACAAGCACAGACTTAATTTAAGGAG
GAAATTAAGTAAGGACAGCACACACTTAATTCAGGAAAATTAAGTAAAG
Found at i:14358 original size:37 final size:37
Alignment explanation
Indices: 14313--14494 Score: 232
Period size: 37 Copynumber: 5.1 Consensus size: 37
14303 TAACCCAAGA
*
14313 GGATTAAGTATAGTAAAGGACTTGATTCCAAGGAAGG
1 GGATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGG
* *
14350 GGATTAAGTAGAGTAAATGACTTAATTCCAAGGAAGG
1 GGATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGG
* **
14387 GAATTAAGTAGAGTTTAGGACTTGATTCCAAGGAAGG
1 GGATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGG
* * *
14424 GGATTAAGTAGAGTTAAGAACTTAATTCCAAGGAAGG
1 GGATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGG
*
14461 GAATTAAGT----T-AAGGACTTGATTCCAAGG-AGG
1 GGATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGG
14492 GGA
1 GGA
14495 ATCAAGTCAA
Statistics
Matches: 129, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
31 5 0.04
32 16 0.12
33 1 0.01
37 107 0.83
ACGTcount: A:0.38, C:0.08, G:0.29, T:0.25
Consensus pattern (37 bp):
GGATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGG
Found at i:14407 original size:74 final size:74
Alignment explanation
Indices: 14315--14494 Score: 266
Period size: 74 Copynumber: 2.5 Consensus size: 74
14305 ACCCAAGAGG
*
14315 ATTAAGTATAGTAAAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTAAATG-ACTTAATTCC
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTAAA-GAACTTAATTCC
14379 AAGGAAGGGA
65 AAGGAAGGGA
** *
14389 ATTAAGTAGAGTTTAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTTAAGAACTTAATTCCA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTAAAGAACTTAATTCCA
14454 AGGAAGGGA
66 AGGAAGGGA
14463 ATTAAGT----T-AAGGACTTGATTCCAAGG-AGGGGA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGGA
14495 ATCAAGTCAA
Statistics
Matches: 100, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
68 6 0.06
69 17 0.17
70 1 0.01
73 1 0.01
74 75 0.75
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.25
Consensus pattern (74 bp):
ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTAAAGAACTTAATTCCA
AGGAAGGGA
Found at i:14516 original size:69 final size:71
Alignment explanation
Indices: 14328--14520 Score: 261
Period size: 74 Copynumber: 2.7 Consensus size: 71
14318 AAGTATAGTA
*
14328 AAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTAAATGACTTAATTCCAAGGAAGGGAATTA
1 AAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTTAA-GACTTAATTCCAAGGAAGGGAATT-
14393 AGTAGAGTT
64 A-TAGAGTT
*
14402 TAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTTAAGAACTTAATTCCAAGGAAGGGAA-T-
1 AAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTTAAG-ACTTAATTCCAAGGAAGGGAATTA
14465 TA-AGTT
65 TAGAGTT
*
14471 AAGGACTTGATTCCAAGG-AGGGGAATCAAGTCA-AGTTAGAGACTTAATTC
1 AAGGACTTGATTCCAAGGAAGGGG-ATTAAGT-AGAGTTA-AGACTTAATTC
14521 GGGGTAATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
68 5 0.05
69 41 0.37
70 5 0.05
73 2 0.02
74 58 0.52
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (71 bp):
AAGGACTTGATTCCAAGGAAGGGGATTAAGTAGAGTTAAGACTTAATTCCAAGGAAGGGAATTAT
AGAGTT
Found at i:14595 original size:36 final size:36
Alignment explanation
Indices: 14510--14642 Score: 205
Period size: 36 Copynumber: 3.7 Consensus size: 36
14500 GTCAAGTTAG
*
14510 AGACTTAATTCGGGGTAATTAAGTAGCGTCAATAAA
1 AGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
*
14546 GGGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
1 -AGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
* *
14583 AGACTTAATTCAGGGTAATTAAGTGGAGTCAAT-AA
1 AGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
14618 AGTACTTAATTCAGGGTAATTAAGT
1 AG-ACTTAATTCAGGGTAATTAAGT
14643 GGAGTTAATA
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
35 4 0.04
36 52 0.58
37 34 0.38
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (36 bp):
AGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA
Found at i:14663 original size:36 final size:36
Alignment explanation
Indices: 14512--14663 Score: 198
Period size: 36 Copynumber: 4.2 Consensus size: 36
14502 CAAGTTAGAG
* * *
14512 ACTTAATTCGGGGTAATTAAGTAGCGTCAATAAAGGG
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAA-GA
*
14549 ACTTAATTCAGGGTAATTAAGTAGCGTCAATAAA-A
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* *
14584 GACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGT
1 -ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* *
14621 ACTTAATTCAGGGTAATTAAGTGGAGTTAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
*
14657 ATTTAAT
1 ACTTAAT
14664 CTAAAAAGAG
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
36 72 0.69
37 33 0.31
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (36 bp):
ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
Found at i:14663 original size:72 final size:73
Alignment explanation
Indices: 14510--14654 Score: 220
Period size: 73 Copynumber: 2.0 Consensus size: 73
14500 GTCAAGTTAG
* * *
14510 AGACTTAATTCGGGGTAATTAAGTAGCGTCAATAAAGGGACTTAATTCAGGGTAATTAAGTAGCG
1 AGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGGGACTTAATTCAGGGTAATTAAGTAGAG
14575 TCAATAAA
66 TCAATAAA
* * *
14583 AGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAA-GTACTTAATTCAGGGTAATTAAGTGGAG
1 AGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGGGACTTAATTCAGGGTAATTAAGTAGAG
*
14647 TTAATAAA
66 TCAATAAA
14655 GAATTTAATC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
72 32 0.49
73 33 0.51
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (73 bp):
AGACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGGGACTTAATTCAGGGTAATTAAGTAGAG
TCAATAAA
Found at i:17802 original size:61 final size:60
Alignment explanation
Indices: 17500--17802 Score: 378
Period size: 60 Copynumber: 5.0 Consensus size: 60
17490 TAAAAAAATC
* * * *
17500 GACGCCACTATATTTAAGGGTTTTTTTTTAAAAAAATCTCAAATTACATATAACGGCG--TA
1 GACGCCGCTATATTTAAGGG--TTTTTTGAAAAAAATCTCAAATTAAATATAGCGGCGTTTA
* *** * *
17560 G-CGGCGTCTATATTTAAGGGTTTTTTTTTTTTAAAAATCTCAAATTACATATAGCAGCGTTTA
1 GACGCCG-CTATATTTAAGGG---TTTTTTGAAAAAAATCTCAAATTAAATATAGCGGCGTTTA
* *
17623 GACGCCGCTATATTTAAGGGTTTTTTGAGAAAAATCTCAAATAAAATATAGCGGCGTTTA
1 GACGCCGCTATATTTAAGGGTTTTTTGAAAAAAATCTCAAATTAAATATAGCGGCGTTTA
* *
17683 GACGCCGCTATATTTAAGGGTTTTTTGAGAAAAATCTCAAATAAAATATAGCGGCGTTTA
1 GACGCCGCTATATTTAAGGGTTTTTTGAAAAAAATCTCAAATTAAATATAGCGGCGTTTA
* *
17743 GACGCTGCTATATTTAAGGGTTTTTTAAAAATAAATCTCAAATTAAATATAGCGGCGTTT
1 GACGCCGCTATATTTAAGGGTTTTTTGAAAA-AAATCTCAAATTAAATATAGCGGCGTTT
17803 CTCGCTATTA
Statistics
Matches: 220, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
59 3 0.01
60 136 0.62
61 61 0.28
63 16 0.07
64 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (60 bp):
GACGCCGCTATATTTAAGGGTTTTTTGAAAAAAATCTCAAATTAAATATAGCGGCGTTTA
Found at i:17886 original size:2 final size:2
Alignment explanation
Indices: 17879--17907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17869 TTTAAATTGA
17879 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 A
17908 AACATTGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18866 original size:3 final size:3
Alignment explanation
Indices: 18858--18892 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
18848 CATAAATGTA
18858 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18893 AAGTAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:33291 original size:31 final size:31
Alignment explanation
Indices: 33247--33323 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
33237 TTAAAATGAG
*
33247 TCAGGGA-TCCAATTGCTCAATTAACTCCACT
1 TCAGGGACTCCAATTGCTC-ACTAACTCCACT
* * *
33278 TCAGGGACT-CAATTGTTCACTAAGTTCACT
1 TCAGGGACTCCAATTGCTCACTAACTCCACT
*
33308 TCAGGGAC-CCATTTGC
1 TCAGGGACTCCAATTGC
33324 ACATTTGCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 22 0.58
31 15 0.39
32 1 0.03
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (31 bp):
TCAGGGACTCCAATTGCTCACTAACTCCACT
Found at i:33380 original size:16 final size:17
Alignment explanation
Indices: 33361--33405 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
33351 GGAATAAAAT
33361 AATTTTTTTTTTT-TTC
1 AATTTTTTTTTTTCTTC
33377 AATTTTTCATTTTTTCTTC
1 AATTTTT--TTTTTTCTTC
33396 -ATTTTTTTTT
1 AATTTTTTTTT
33406 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 11 0.42
18 12 0.46
19 3 0.12
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (17 bp):
AATTTTTTTTTTTCTTC
Found at i:33414 original size:11 final size:11
Alignment explanation
Indices: 33379--33416 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
33369 TTTTTTTCAA
33379 TTTTTCATTTT
1 TTTTTCATTTT
*
33390 TTCTTCATTTT
1 TTTTTCATTTT
*
33401 TTTTTCCTTTT
1 TTTTTCATTTT
33412 TTTTT
1 TTTTT
33417 AAATCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:34198 original size:19 final size:19
Alignment explanation
Indices: 34173--34211 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
34163 CCTTAACCCA
34173 ATTTTTTT--TAAAAAATAT
1 ATTTTTTTAATAAAAAA-AT
34191 ATTTTTTTAATAAAAAAAT
1 ATTTTTTTAATAAAAAAAT
34210 AT
1 AT
34212 GATGTGGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 4 0.21
20 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTTTTTAATAAAAAAAT
Found at i:34845 original size:30 final size:29
Alignment explanation
Indices: 34809--34883 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 29
34799 TGTTGTGCTC
34809 ATAGTTTAGCTTAGCTAAATTTGATTGTAA
1 ATAGTTTAGCTTAGCTAAATTTGATTGT-A
*
34839 ATAGTTTACCTTAGCTAAATTTGATTGTA
1 ATAGTTTAGCTTAGCTAAATTTGATTGTA
34868 ATATGTTT-GC-TAGCTA
1 ATA-GTTTAGCTTAGCTA
34884 TGTGCGGTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 6 0.14
29 5 0.12
30 31 0.74
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (29 bp):
ATAGTTTAGCTTAGCTAAATTTGATTGTA
Found at i:37895 original size:40 final size:40
Alignment explanation
Indices: 37751--38037 Score: 253
Period size: 47 Copynumber: 6.9 Consensus size: 40
37741 TGGGTTCCAA
*
37751 TTTCCCA-TTCTGCCCTTCCCCACCGGAA-G-G-TG--TAG
1 TTTCCCAGTT-TGCCCTTCCCCATCGGAAGGTGTTGTTTAG
* * * *
37786 TTTCTCAGTCTGCCCTTCCCCGTCGGAAGGTGTTGTTTACA
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA-G
* *
37827 TTTCTCACTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG
* **
37867 TTTCCCAGTTTGTCCTTCCCGGTCGGAAGGTGTTGTTTAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG
* * *
37907 TTTCTCAGTTTACCCTTCCCCACCGGAAGGTGTTGTTTAAG
1 TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG
*
37948 TCTATTTTTCCCAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTAAG
1 ------TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG
*
37995 TCTATTTTTCCCAGTTTGCCCTTCCCTATCGGAAGGTGTTGTT
1 ------TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTT
38038 ATCTTTACTT
Statistics
Matches: 214, Mismatches: 24, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
35 22 0.10
36 2 0.01
37 1 0.00
38 2 0.01
40 69 0.32
41 38 0.18
47 80 0.37
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.39
Consensus pattern (40 bp):
TTTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAG
Found at i:38116 original size:50 final size:50
Alignment explanation
Indices: 38049--38390 Score: 422
Period size: 50 Copynumber: 6.9 Consensus size: 50
38039 TCTTTACTTA
* * *
38049 TTCCAAAAATCCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGT
* * *
38099 TTCCCAAAATGCCCCTTCCCGGTCGAAAGGTCCCTGTTTT-TTCTGTCTGT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTT-TGTTTGT
** * *
38149 TTACC-AAAATGCCCCTTCTTGGTCGGAAGGTCTCTGTTTCCTTTGTTTGT
1 TT-CCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGT
* * * *
38199 TTCCGAAAATGCCCCTTCCCGGTTGGAAGGTCCCTGTTTTCTTTATTT-A
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGT
* * * *
38248 TTCCAAAAATGCCTCTTCCTGGTTGGAAGGTCCCTGTTTCCTTTGTTTGT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGT
* *
38298 TTCCAAAAATGCCCCTTCCCGGTCGGGAGGTCCCTGTTTTCTTTATTTG-
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGT
* * * *
38347 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTGTTTCCTTT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTT
38391 ATTT
Statistics
Matches: 251, Mismatches: 36, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
49 86 0.34
50 161 0.64
51 4 0.02
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (50 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTTCTTTGTTTGT
Found at i:38297 original size:99 final size:99
Alignment explanation
Indices: 38034--38390 Score: 477
Period size: 99 Copynumber: 3.6 Consensus size: 99
38024 CGGAAGGTGT
* * * * * * *
38034 TGTTATCTTTACTTATTCCAAAAATCCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTTTGC
1 TGTTTTCTTTATTTATTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTGTTTGT
* *
38099 TTCCCAAAATGCCCCTTCCCGGTCGAAAGGTCCC
66 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCC
* * *
38133 TGTTTT-TTCTGTCTGT-TTACC-AAAATGCCCCTTCTTGGTCGGAAGGTCTCTGTTTCCTTTGT
1 TGTTTTCTT-TAT-T-TATT-CCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTGT
* *
38195 TTGTTTCCGAAAATGCCCCTTCCCGGTTGGAAGGTCCC
62 TTGTTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCC
* *
38233 TGTTTTCTTTATTTATTCCAAAAATGCCTCTTCCTGGTTGGAAGGTCCCTGTTTCCTTTGTTTGT
1 TGTTTTCTTTATTTATTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTGTTTGT
*
38298 TTCCAAAAATGCCCCTTCCCGGTCGGGAGGTCCC
66 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCC
* * *
38332 TGTTTTCTTTATTTGTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCACTGTTTCCTTT
1 TGTTTTCTTTATTTATTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTT
38391 ATTT
Statistics
Matches: 227, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
98 5 0.02
99 137 0.60
100 80 0.35
101 5 0.02
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.39
Consensus pattern (99 bp):
TGTTTTCTTTATTTATTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTGTTTGT
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCC
Done.