Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011696.1 Corchorus capsularis cultivar CVL-1 contig11717, 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: 39877
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2797 original size:14 final size:13
Alignment explanation
Indices: 2775--2825 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
2765 CAAGAAACGT
*
2775 TTTTCAAAAATTG
1 TTTTCAAAAATAG
*
2788 TTTTCAAAAAATGG
1 TTTTC-AAAAATAG
*
2802 TTTTCAGAAATGAG
1 TTTTCAAAAAT-AG
2816 TTTTCAAAAA
1 TTTTCAAAAA
2826 GGTTTTTGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:3468 original size:11 final size:11
Alignment explanation
Indices: 3452--3493 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
3442 CATTCAACTC
3452 AAAG-AAAAGAA
1 AAAGAAAAAG-A
3463 AAAGAAAAA-A
1 AAAGAAAAAGA
3473 GAAAGAAAAAGA
1 -AAAGAAAAAGA
3485 AAAGAAAAA
1 AAAGAAAAA
3494 AACTTGGCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 22 0.79
12 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:3479 original size:17 final size:18
Alignment explanation
Indices: 3452--3487 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3442 CATTCAACTC
3452 AAAGAAAAGAAAAAGAAA
1 AAAGAAAAGAAAAAGAAA
3470 AAAG-AAAGAAAAAGAAA
1 AAAGAAAAGAAAAAGAAA
3487 A
1 A
3488 GAAAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAAAAGAAA
Found at i:3480 original size:22 final size:22
Alignment explanation
Indices: 3452--3494 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3442 CATTCAACTC
3452 AAAG-AAAAGAAAAAGAAAAAAG
1 AAAGAAAAAG-AAAAGAAAAAAG
3474 AAAGAAAAAGAAAAGAAAAAA
1 AAAGAAAAAGAAAAGAAAAAA
3495 ACTTGGCCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAGAAAAGAAAAAAG
Found at i:5182 original size:54 final size:54
Alignment explanation
Indices: 5107--5283 Score: 203
Period size: 54 Copynumber: 3.3 Consensus size: 54
5097 AGAGATAGTC
* * * *
5107 TCAAGTGATCTACTGCGGTCAATCAAGAAAGTTTCCAGTGGCTTAAGTTTATCT
1 TCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
* * * *
5161 TTAAGTGATCCAGTGCAGTCAATCCAGAAAGTCTCCAGTGGTTTAAGTGTATCT
1 TCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
* * ** * *
5215 TCAAGTGATCCAGTG-TGAACAATCAAGAAAGTTTCTGGTGATTTAAGTTCATCT
1 TCAAGTGATCCAGTGCAG-TCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
*
5269 TCAAGTAATCCAGTG
1 TCAAGTGATCCAGTG
5284 AACATCTTTC
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
53 1 0.01
54 102 0.99
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
TCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATCT
Found at i:5326 original size:36 final size:36
Alignment explanation
Indices: 5286--5585 Score: 330
Period size: 36 Copynumber: 8.4 Consensus size: 36
5276 ATCCAGTGAA
*
5286 CATCTTTCAAAGTTGATTTCAGATGACTCAGTGTAG
1 CATCTTTCAAAGTTGATTTCAGATGACTCGGTGTAG
* *
5322 CATCTTTCAAAGTTGGTTTCAAATGA-TGCGGTGTAG
1 CATCTTTCAAAGTTGATTTCAGATGACT-CGGTGTAG
*
5358 CATCTTTCAAAGTTGGTTTCAGATGACTCGGTGTAG
1 CATCTTTCAAAGTTGATTTCAGATGACTCGGTGTAG
5394 CATC-TTCAAAGTTGGA-TTCAGATGACTCGGTGTAG
1 CATCTTTCAAAGTT-GATTTCAGATGACTCGGTGTAG
*
5429 CATC-TTCAAAGTTGGA-TTCGGATGACTCGGTGTAG
1 CATCTTTCAAAGTT-GATTTCAGATGACTCGGTGTAG
* * *
5464 CACCTTTCAAAGTTGGTTCCAGATGACGT-GGTGTAG
1 CATCTTTCAAAGTTGATTTCAGATGAC-TCGGTGTAG
* * * ** *
5500 CATCTTTCAAAGATGGTTTCAGACGACTTAGTGCAG
1 CATCTTTCAAAGTTGATTTCAGATGACTCGGTGTAG
* *
5536 CATC-TTCAAAAGTTGGA-TTGAGATGACTCGGTGAAG
1 CATCTTTC-AAAGTT-GATTTCAGATGACTCGGTGTAG
*
5572 CATC-TCCAAAGTTG
1 CATCTTTCAAAGTTG
5586 GATTAGGTGA
Statistics
Matches: 231, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.00
35 77 0.33
36 150 0.65
37 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (36 bp):
CATCTTTCAAAGTTGATTTCAGATGACTCGGTGTAG
Found at i:5471 original size:142 final size:143
Alignment explanation
Indices: 5281--5589 Score: 444
Period size: 142 Copynumber: 2.2 Consensus size: 143
5271 AAGTAATCCA
* *
5281 GTGAA-CATCTTTCAAAGTT-GATTTCAGATGACTCAGTGTAGCATCTTTCAAAGTTGGTTTCAA
1 GTGAAGCATC-TTCAAAGTTGGA-TTCAGATGACTCAGTGTAGCACCTTTCAAAGTTGGTTCCAA
* * * * *
5344 ATGATGCGGTGTAGCATCTTTCAAAGTTGGTTTCAGATGACTCGGTGTAGCATCTTC-AAAGTTG
64 ATGACGCGGTGTAGCATCTTTCAAAGATGGTTTCAGACGACTCAGTGCAGCATCTTCAAAAGTTG
5408 GATTCAGATGACTCG
129 GATTCAGATGACTCG
* * * *
5423 GTGTAGCATCTTCAAAGTTGGATTCGGATGACTCGGTGTAGCACCTTTCAAAGTTGGTTCCAGAT
1 GTGAAGCATCTTCAAAGTTGGATTCAGATGACTCAGTGTAGCACCTTTCAAAGTTGGTTCCAAAT
* *
5488 GACGTGGTGTAGCATCTTTCAAAGATGGTTTCAGACGACTTAGTGCAGCATCTTCAAAAGTTGGA
66 GACGCGGTGTAGCATCTTTCAAAGATGGTTTCAGACGACTCAGTGCAGCATCTTCAAAAGTTGGA
*
5553 TTGAGATGACTCG
131 TTCAGATGACTCG
*
5566 GTGAAGCATCTCCAAAGTTGGATT
1 GTGAAGCATCTTCAAAGTTGGATT
5590 AGGTGAACCA
Statistics
Matches: 148, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
142 99 0.67
143 49 0.33
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (143 bp):
GTGAAGCATCTTCAAAGTTGGATTCAGATGACTCAGTGTAGCACCTTTCAAAGTTGGTTCCAAAT
GACGCGGTGTAGCATCTTTCAAAGATGGTTTCAGACGACTCAGTGCAGCATCTTCAAAAGTTGGA
TTCAGATGACTCG
Found at i:5939 original size:91 final size:91
Alignment explanation
Indices: 5624--6414 Score: 1110
Period size: 91 Copynumber: 8.7 Consensus size: 91
5614 GCATTTTCTT
* * * * * *
5624 TTTC-TCAAGATTGGATTCAGTGAGCTCGGTGCAGCAGATTTTCAAATAGTTCAAGATCATTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
* *
5688 TGAATCAAG-TAGGGGCGGTGCCTTA
66 TGAATCAAGATTGAGGCGGTGCCTTA
* * * * * *
5713 CTTCTTCAA-AGTCAGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAATAGTTCAAGATCATTCG
1 TTTCTTCAAGA-TCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCG
*
5777 GTGAATCAAG--TGGGGCCGGTGCCTTA
65 GTGAATCAAGATTGAGG-CGGTGCCTTA
* * * * * *
5803 CTTCTTCAA-AGCCAGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAGGATGATTCG
1 TTTCTTCAAGA-TCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCG
5867 GTGAATCAAGATTG-GGACGGTGCCTTA
65 GTGAATCAAGATTGAGG-CGGTGCCTTA
* * * *
5894 TTTCTTCCAGATCGGGTTCGGTGAGCTCGGAGCAACATATTTTCAAATAGTTCAAGATGATTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
*
5959 TGAATCAAGATTGAGGTGGTGCCTTA
66 TGAATCAAGATTGAGGCGGTGCCTTA
* * * *
5985 TTTCTTCCAGATCGGGTTCGGTGAGCTCGGTGCATCATATTTTCAAATAGTTCAAGATGATTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
6050 TGAATCAAGATTGAGGCGGTGCCTTA
66 TGAATCAAGATTGAGGCGGTGCCTTA
*
6076 TTTCTTCAAGATCAGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
*
6141 TGAATCAAGATTAAGGCGGTGCCTTA
66 TGAATCAAGATTGAGGCGGTGCCTTA
* * * * *
6167 TTTATTCAAGATTGGATTCGGTGAACTCGGTGCAGCATATTTTCAAATAGTTCAGGATGACTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
6232 TGAATCAAGATTGAGGCGGTGCCTTA
66 TGAATCAAGATTGAGGCGGTGCCTTA
* *
6258 TTTCTTCAAGATTGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCTGGATGATTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
*
6323 TGAATCAAGATTGAGGCGGTGCCTTT
66 TGAATCAAGATTGAGGCGGTGCCTTA
* * *
6349 TTTCTTCAAGATTGGATTCGATGAGCTCGGTGCAACACATTTTCAAATAGTTCAGGATGATTCGG
1 TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
6414 T
66 T
6415 CGTTTCCATA
Statistics
Matches: 649, Mismatches: 46, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
89 8 0.01
90 144 0.22
91 492 0.76
92 5 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (91 bp):
TTTCTTCAAGATCGGATTCGGTGAGCTCGGTGCAACATATTTTCAAATAGTTCAGGATGATTCGG
TGAATCAAGATTGAGGCGGTGCCTTA
Found at i:6523 original size:68 final size:68
Alignment explanation
Indices: 6414--6661 Score: 394
Period size: 67 Copynumber: 3.6 Consensus size: 68
6404 GATGATTCGG
*
6414 TCGTTTCCATACGA-TGCAGTTTAGCCTTGGTTCCATCCAAGCAAAAGAGGCTTTTCCACAAGCC
1 TCGTTTCCACACGAGT-CAGTTTAGCCTTGGTTCCATCCAAGCAAAAGAGGCTTTTCCACAAGCC
6478 AAAC
65 AAAC
6482 TCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAAAAGAGG-TTTTCCACAAGCCA
1 TCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAAAAGAGGCTTTTCCACAAGCCA
6546 AAC
66 AAC
* *
6549 TCGTTTCCACACGAGTCAGTTTAGCTTTGGTTCCATCCAAGCATTCAA-AGGCTTTTCCACAAGC
1 TCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCA--AAAGAGGCTTTTCCACAAGC
6613 CAAAC
64 CAAAC
**
6618 TCGTTTCCACACGAGTCAGTTTAAGATTTGGTTCCATCCAAGCA
1 TCGTTTCCACACGAGTCAGTTT-AGCCTTGGTTCCATCCAAGCA
6662 TTTAGGGGCA
Statistics
Matches: 171, Mismatches: 4, Indels: 8
0.93 0.02 0.04
Matches are distributed among these distances:
67 59 0.35
68 50 0.29
69 42 0.25
70 20 0.12
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (68 bp):
TCGTTTCCACACGAGTCAGTTTAGCCTTGGTTCCATCCAAGCAAAAGAGGCTTTTCCACAAGCCA
AAC
Found at i:6921 original size:96 final size:96
Alignment explanation
Indices: 6799--7129 Score: 558
Period size: 96 Copynumber: 3.5 Consensus size: 96
6789 CCAGACAATC
* *
6799 TTCTCTCGCTTCCACGCGAGTTTTCAATTCGGTGGCCAAAGTTGGCATTCTCTCTCGCTTACACG
1 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCATTCTCTCTCGCTTCCACG
6864 CGAGTTAACAATTCAGTGGCCAAAGTTGGCA
66 CGAGTTAACAATTCAGTGGCCAAAGTTGGCA
*
6895 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCATTCTCTATCGCTTCCACG
1 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCATTCTCTCTCGCTTCCACG
*
6960 CGAGTTAACAATTCAGTGGCCAAAGTTGGTA
66 CGAGTTAACAATTCAGTGGCCAAAGTTGGCA
*
6991 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCA-T-TCTCTCGCTTCCAGG
1 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCATTCTCTCTCGCTTCCACG
*
7054 CGAGTTAGCAATTCAGTGGCCAAAGTTGGCA
66 CGAGTTAACAATTCAGTGGCCAAAGTTGGCA
** * *
7085 TTCTCTCGCTTCCACGCGAGTTGGCAATTTAGTGACCAAAGTTGG
1 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGG
7130 TCAGCGGGTT
Statistics
Matches: 223, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
94 83 0.37
95 1 0.00
96 139 0.62
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (96 bp):
TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCATTCTCTCTCGCTTCCACG
CGAGTTAACAATTCAGTGGCCAAAGTTGGCA
Found at i:6923 original size:47 final size:47
Alignment explanation
Indices: 6799--7129 Score: 500
Period size: 47 Copynumber: 7.0 Consensus size: 47
6789 CCAGACAATC
* *
6799 TTCTCTCGCTTCCACGCGAGTTTTCAATTCGGTGGCCAAAGTTGGCA
1 TTCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
* *
6846 TTCTCTCTCGCTTACACGCGAGTTAACAATTCAGTGGCCAAAGTTGGCA
1 -T-TCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
*
6895 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCA
1 TTCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
* *
6942 TTCTCTATCGCTTCCACGCGAGTTAACAATTCAGTGGCCAAAGTTGGTA
1 TTCTC--TCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
*
6991 TTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCA
1 TTCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
* *
7038 TTCTCTCGCTTCCAGGCGAGTTAGCAATTCAGTGGCCAAAGTTGGCA
1 TTCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
** * *
7085 TTCTCTCGCTTCCACGCGAGTTGGCAATTTAGTGACCAAAGTTGG
1 TTCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGG
7130 TCAGCGGGTT
Statistics
Matches: 260, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
47 172 0.66
48 2 0.01
49 86 0.33
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (47 bp):
TTCTCTCGCTTCCACGCGAGTTATCAATTCAGTGGCCAAAGTTGGCA
Found at i:7057 original size:143 final size:143
Alignment explanation
Indices: 6799--7130 Score: 506
Period size: 143 Copynumber: 2.3 Consensus size: 143
6789 CCAGACAATC
** * *
6799 TTCTCTCGCTTCCACGCGAGTTTTCAATTCGGTGGCCAAAGTTGGCATTCTCTCTCGCTTACACG
1 TTCTCTCGCTTCCACGCGAGTTAACAATTCAGTGGCCAAAGTTGGTATTCTCTCTCGCTTACACG
**
6864 CGAGTTAACAATTCAGTGGCCAAAGTTGGCATTCTCTCGCTTCCACGCGAGTTTTCAATTCAGTG
66 CGAGTTAACAATTCAGTGGCCAAAGTTGGCATTCTCTCGCTTCCACGCGAGTTAGCAATTCAGTG
6929 GCCAAAGTTGGCA
131 GCCAAAGTTGGCA
*
6942 TTCTCTATCGCTTCCACGCGAGTTAACAATTCAGTGGCCAAAGTTGGTA-T-TCTCTCGCTTCCA
1 TTCTC--TCGCTTCCACGCGAGTTAACAATTCAGTGGCCAAAGTTGGTATTCTCTCTCGCTTACA
** *
7005 CGCGAGTTTTCAATTCAGTGGCCAAAGTTGGCATTCTCTCGCTTCCAGGCGAGTTAGCAATTCAG
64 CGCGAGTTAACAATTCAGTGGCCAAAGTTGGCATTCTCTCGCTTCCACGCGAGTTAGCAATTCAG
7070 TGGCCAAAGTTGGCA
129 TGGCCAAAGTTGGCA
** * *
7085 TTCTCTCGCTTCCACGCGAGTTGGCAATTTAGTGACCAAAGTTGGT
1 TTCTCTCGCTTCCACGCGAGTTAACAATTCAGTGGCCAAAGTTGGT
7131 CAGCGGGTTT
Statistics
Matches: 173, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
141 37 0.21
143 97 0.56
144 1 0.01
145 38 0.22
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (143 bp):
TTCTCTCGCTTCCACGCGAGTTAACAATTCAGTGGCCAAAGTTGGTATTCTCTCTCGCTTACACG
CGAGTTAACAATTCAGTGGCCAAAGTTGGCATTCTCTCGCTTCCACGCGAGTTAGCAATTCAGTG
GCCAAAGTTGGCA
Found at i:7200 original size:10 final size:10
Alignment explanation
Indices: 7185--7223 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
7175 AGTCTTAAAA
7185 AAAAACAAAC
1 AAAAACAAAC
7195 AAAAACAAAC
1 AAAAACAAAC
*
7205 AAAAAAAAAC
1 AAAAACAAAC
7215 AAAAACAAA
1 AAAAACAAA
7224 AACAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAC
Found at i:7202 original size:6 final size:6
Alignment explanation
Indices: 7191--7231 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
7181 AAAAAAAAAC
*
7191 AAACAA AAACAAA CAAAAAA AAACAA AAACAA AAACAA AAA
1 AAACAA AAAC-AA -AAACAA AAACAA AAACAA AAACAA AAA
7232 AGGAGAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 24 0.77
7 4 0.13
8 3 0.10
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:7214 original size:20 final size:19
Alignment explanation
Indices: 7181--7232 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
7171 GATTAGTCTT
7181 AAAAAAAAACAAACAAAAAC
1 AAAAAAAAA-AAACAAAAAC
7201 AAACAAAAAAAAACAAAAAC
1 AAA-AAAAAAAAACAAAAAC
7221 AAAAACAAAAAA
1 AAAAA-AAAAAA
7233 GGAGAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 22 0.73
21 6 0.20
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAACAAAAAC
Found at i:7220 original size:26 final size:24
Alignment explanation
Indices: 7181--7232 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
7171 GATTAGTCTT
7181 AAAAAAAAACAAACAAAAACAAAC
1 AAAAAAAAACAAACAAAAACAAAC
*
7205 AAAAAAAAACAAA-AACAA-AAAC
1 AAAAAAAAACAAACAAAAACAAAC
7227 AAAAAA
1 AAAAAA
7233 GGAGAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.37
23 4 0.15
24 13 0.48
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAAAAACAAACAAAAACAAAC
Found at i:7245 original size:26 final size:26
Alignment explanation
Indices: 7181--7229 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
7171 GATTAGTCTT
7181 AAAAAAAAAC--AAACAAAAACAAAC
1 AAAAAAAAACAAAAACAAAAACAAAC
7205 AAAAAAAAACAAAAACAAAAACAAA
1 AAAAAAAAACAAAAACAAAAACAAA
7230 AAAGGAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.43
26 13 0.57
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (26 bp):
AAAAAAAAACAAAAACAAAAACAAAC
Found at i:16656 original size:32 final size:32
Alignment explanation
Indices: 16610--16686 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
16600 CCATGGCGAA
**
16610 GCCGCCCCACTGGGGCAGCTTAGCCACGGCAG
1 GCCGCCCCGGTGGGGCAGCTTAGCCACGGCAG
* *
16642 GCCGCCCCGGTGGGGCGGCTTCGCCACGGCAG
1 GCCGCCCCGGTGGGGCAGCTTAGCCACGGCAG
*
16674 GCCGCCTCGGTGG
1 GCCGCCCCGGTGG
16687 AGCGGCTCGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.09, C:0.40, G:0.40, T:0.10
Consensus pattern (32 bp):
GCCGCCCCGGTGGGGCAGCTTAGCCACGGCAG
Found at i:16692 original size:32 final size:32
Alignment explanation
Indices: 16627--16693 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
16617 CACTGGGGCA
*
16627 GCTTAGCCACGGCAGGCCGCCCCGGTGGGGCG
1 GCTTAGCCACGGCAGGCCGCCCCGGTGGAGCG
* *
16659 GCTTCGCCACGGCAGGCCGCCTCGGTGGAGCG
1 GCTTAGCCACGGCAGGCCGCCCCGGTGGAGCG
16691 GCT
1 GCT
16694 CGGCTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.09, C:0.37, G:0.42, T:0.12
Consensus pattern (32 bp):
GCTTAGCCACGGCAGGCCGCCCCGGTGGAGCG
Found at i:16815 original size:32 final size:32
Alignment explanation
Indices: 16767--16827 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
16757 CGTTCCACCG
16767 GGGCGGCCTGCCGTGGCAAAGCCACCCCATGA
1 GGGCGGCCTGCCGTGGCAAAGCCACCCCATGA
* * * *
16799 GGGCGGCTTGCTGTGGCGAAGCCGCCCCA
1 GGGCGGCCTGCCGTGGCAAAGCCACCCCA
16828 GTGGGGAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.15, C:0.36, G:0.38, T:0.11
Consensus pattern (32 bp):
GGGCGGCCTGCCGTGGCAAAGCCACCCCATGA
Found at i:16942 original size:21 final size:21
Alignment explanation
Indices: 16918--16958 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16908 CAAAAGTATA
16918 AAAAATAGGACAATATTTAGT
1 AAAAATAGGACAATATTTAGT
* **
16939 AAAACTAGGACGGTATTTAG
1 AAAAATAGGACAATATTTAG
16959 CAACCCCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (21 bp):
AAAAATAGGACAATATTTAGT
Found at i:30254 original size:18 final size:18
Alignment explanation
Indices: 30231--30268 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30221 TCCTAGGAAA
30231 CACTTGTATAGAACACAT
1 CACTTGTATAGAACACAT
30249 CACTTGTATAGAACACAT
1 CACTTGTATAGAACACAT
30267 CA
1 CA
30269 TGACATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (18 bp):
CACTTGTATAGAACACAT
Found at i:33636 original size:15 final size:15
Alignment explanation
Indices: 33616--33647 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
33606 TAGTACTATC
33616 TTTTTTTTCTTTGAT
1 TTTTTTTTCTTTGAT
33631 TTTTTTTTCTTTGAT
1 TTTTTTTTCTTTGAT
33646 TT
1 TT
33648 GATAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTTTTCTTTGAT
Found at i:38036 original size:5 final size:5
Alignment explanation
Indices: 38026--38101 Score: 92
Period size: 5 Copynumber: 16.4 Consensus size: 5
38016 TATTAGTTGA
* *
38026 TATCT TATCT TATCT TA-C- TATTT TATCT TA-C- TATCT TA-C- CATCT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
38070 TATCT TATCT TATCT TATCT TATCT TATCT TA
1 TATCT TATCT TATCT TATCT TATCT TATCT TA
38102 CAACTATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
3 5 0.08
4 5 0.08
5 51 0.84
ACGTcount: A:0.22, C:0.21, G:0.00, T:0.57
Consensus pattern (5 bp):
TATCT
Found at i:38053 original size:13 final size:13
Alignment explanation
Indices: 38035--38059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38025 ATATCTTATC
38035 TTATCTTACTATT
1 TTATCTTACTATT
38048 TTATCTTACTAT
1 TTATCTTACTAT
38060 CTTACCATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATCTTACTATT
Done.