Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015293.1 Corchorus capsularis cultivar CVL-1 contig15314, 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: 20024
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:5018 original size:6 final size:6
Alignment explanation
Indices: 5007--5035 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4997 CCTTAGCTCC
5007 TTCACA TTCACA TTCACA TTCACA TTCAC
1 TTCACA TTCACA TTCACA TTCACA TTCAC
5036 CACCCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (6 bp):
TTCACA
Found at i:9154 original size:30 final size:31
Alignment explanation
Indices: 9113--9260 Score: 104
Period size: 30 Copynumber: 4.7 Consensus size: 31
9103 AACCGCTGAA
*
9113 ATGGCAATGCCACGT-GGCATTTTGCGCCAC
1 ATGGCATTGCCACGTCGGCATTTTGCGCCAC
* *
9143 ATGGCATTGCCACGTCAGCATCTTGTCGACC-C
1 ATGGCATTGCCACGTCGGCATTTTG-CG-CCAC
* ***** * *
9175 ATGTGGCATTGCCATGTCGGACAAAAACCGCTGAA
1 A--TGGCATTGCCACGTCGG-CATTTTGCGC-CAC
*
9210 ATGGCAATGCCACGT-GGCATTTTGCGCCAC
1 ATGGCATTGCCACGTCGGCATTTTGCGCCAC
*
9240 ATGGCATTGCCACGTCAGCAT
1 ATGGCATTGCCACGTCGGCAT
9261 CTTGACGGTG
Statistics
Matches: 86, Mismatches: 23, Indels: 17
0.68 0.18 0.13
Matches are distributed among these distances:
30 29 0.34
31 16 0.19
32 6 0.07
33 15 0.17
34 17 0.20
35 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (31 bp):
ATGGCATTGCCACGTCGGCATTTTGCGCCAC
Found at i:9255 original size:97 final size:97
Alignment explanation
Indices: 9089--9264 Score: 352
Period size: 97 Copynumber: 1.8 Consensus size: 97
9079 TTTTTTAATA
9089 CCATGTCGGACAAAAACCGCTGAAATGGCAATGCCACGTGGCATTTTGCGCCACATGGCATTGCC
1 CCATGTCGGACAAAAACCGCTGAAATGGCAATGCCACGTGGCATTTTGCGCCACATGGCATTGCC
9154 ACGTCAGCATCTTGTCGACCCATGTGGCATTG
66 ACGTCAGCATCTTGTCGACCCATGTGGCATTG
9186 CCATGTCGGACAAAAACCGCTGAAATGGCAATGCCACGTGGCATTTTGCGCCACATGGCATTGCC
1 CCATGTCGGACAAAAACCGCTGAAATGGCAATGCCACGTGGCATTTTGCGCCACATGGCATTGCC
9251 ACGTCAGCATCTTG
66 ACGTCAGCATCTTG
9265 ACGGTGTCGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (97 bp):
CCATGTCGGACAAAAACCGCTGAAATGGCAATGCCACGTGGCATTTTGCGCCACATGGCATTGCC
ACGTCAGCATCTTGTCGACCCATGTGGCATTG
Found at i:9332 original size:29 final size:29
Alignment explanation
Indices: 9285--9359 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
9275 TAGCTTGAGG
*
9285 GGGCAAAACGTCCCAAAATTGAAGTTTAT-
1 GGGCAAAACGT-CCAAAATTGAAGTTCATA
*
9314 GAGGCAAAATGTCCAAAATTGAAGTTCATA
1 G-GGCAAAACGTCCAAAATTGAAGTTCATA
9344 GGGCAAAACGTCCAAA
1 GGGCAAAACGTCCAAA
9360 CGCTACAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 31 0.76
30 10 0.24
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.20
Consensus pattern (29 bp):
GGGCAAAACGTCCAAAATTGAAGTTCATA
Found at i:9716 original size:2 final size:2
Alignment explanation
Indices: 9711--9761 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
9701 TATATATATA
* * *
9711 TG TG TG TG TG TG TG TG TG TC TG TG TC TG TG TC TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9753 TG TG TG TG T
1 TG TG TG TG T
9762 ACCAAGTAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.06, G:0.43, T:0.51
Consensus pattern (2 bp):
TG
Found at i:15457 original size:19 final size:19
Alignment explanation
Indices: 15435--15492 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
15425 TTCAACGTCC
15435 TATTTAATTTTGCCTTTTG
1 TATTTAATTTTGCCTTTTG
*
15454 TATTT--GTTT-CCAATTGTTG
1 TATTTAATTTTGCC--TT-TTG
*
15473 TATTTAATTTTGCTTTTTG
1 TATTTAATTTTGCCTTTTG
15492 T
1 T
15493 TTTTGTCTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 12
0.67 0.07 0.27
Matches are distributed among these distances:
16 2 0.07
17 3 0.10
18 2 0.07
19 17 0.57
20 2 0.07
21 3 0.10
22 1 0.03
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.64
Consensus pattern (19 bp):
TATTTAATTTTGCCTTTTG
Found at i:15998 original size:19 final size:20
Alignment explanation
Indices: 15971--16008 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
15961 TACTATTATT
15971 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
15991 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
16009 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:16202 original size:22 final size:22
Alignment explanation
Indices: 16174--16258 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
16164 TGTCTCTATG
16174 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
16196 TGGTTATTATAATTTCACGAGGA
1 TGGTTATCAAAATTTCA-TAAGA
* * *
16219 -GGTTATCGAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
16240 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
16259 GGACCAGGTT
Statistics
Matches: 45, Mismatches: 14, Indels: 7
0.68 0.21 0.11
Matches are distributed among these distances:
20 1 0.02
22 41 0.91
23 3 0.07
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:16293 original size:22 final size:22
Alignment explanation
Indices: 16265--16306 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16255 CATAGGACCA
*
16265 GGTTATT-ACAATTTCTTAGGTT
1 GGTTATTGA-AATTTCATAGGTT
16287 GGTTATTGAAATTTCATAGG
1 GGTTATTGAAATTTCATAGG
16307 GTGATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.45
Consensus pattern (22 bp):
GGTTATTGAAATTTCATAGGTT
Found at i:16370 original size:22 final size:22
Alignment explanation
Indices: 16345--16387 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16335 GATTATCAAA
16345 GAGATTATCAA-AATGTCATAGC
1 GAGATTAT-AAGAATGTCATAGC
*
16367 GAGATTATAAGAATTTCATAG
1 GAGATTATAAGAATGTCATAG
16388 TGTGGTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
GAGATTATAAGAATGTCATAGC
Found at i:16403 original size:22 final size:22
Alignment explanation
Indices: 16378--16474 Score: 92
Period size: 22 Copynumber: 4.4 Consensus size: 22
16368 AGATTATAAG
16378 AATTTCATAGTGTGGTTAACAA
1 AATTTCATAGTGTGGTTAACAA
16400 AATTTCATTAG-GTGGTT-ACTAA
1 AATTTCA-TAGTGTGGTTAAC-AA
* * * *
16422 TATTTCAT-GGGCAGGTTATCAA
1 AATTTCATAGTG-TGGTTAACAA
* *
16444 AATTTTATAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTAACAA
16466 AATTTCATA
1 AATTTCATA
16475 TGAAGATTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 4 0.07
22 50 0.82
23 6 0.10
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTAACAA
Found at i:16484 original size:22 final size:22
Alignment explanation
Indices: 16437--16676 Score: 102
Period size: 22 Copynumber: 10.7 Consensus size: 22
16427 CATGGGCAGG
* * *
16437 TTATCAAAATTTTATAGTG-TGG
1 TTATCAAAATTTCATA-TGAAGA
16459 TTATCAAAATTTCATATGAAGA
1 TTATCAAAATTTCATATGAAGA
* *
16481 TTAT-AAAAGTCTCAATTTCATAAAGA
1 TTATCAAAA-TTTC-A--T-ATGAAGA
* * * *
16507 GTACCAAAATTTGATA-GAAGG
1 TTATCAAAATTTCATATGAAGA
* *
16528 TTATC-AAATCTCATA-GAGTGA
1 TTATCAAAATTTCATATGA-AGA
* *
16549 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATA-TGA--AGA
* *
16574 TTATCAAAATTT-ATAGGAAGC
1 TTATCAAAATTTCATATGAAGA
**
16595 TTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATA-TGAAGA
* *
16617 TTATCAAAATTTCA-AAGCAAGG
1 TTATCAAAATTTCATATG-AAGA
* *
16639 TTATCAAAATTACATAATG-TGA
1 TTATCAAAATTTCAT-ATGAAGA
*
16661 TTATCAGAATTTCATA
1 TTATCAAAATTTCATA
16677 GAGGGGTCAA
Statistics
Matches: 165, Mismatches: 35, Indels: 37
0.70 0.15 0.16
Matches are distributed among these distances:
20 11 0.07
21 35 0.21
22 77 0.47
23 6 0.04
24 7 0.04
25 15 0.09
26 10 0.06
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATATGAAGA
Found at i:16665 original size:44 final size:44
Alignment explanation
Indices: 16572--16762 Score: 160
Period size: 44 Copynumber: 4.4 Consensus size: 44
16562 ATAGAGATCA
* * *
16572 GATTATCAAAATTT-ATAG-GAAGCTTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAG-AGGTTATCAAAATTTCATAATG-T
*
16616 G-TTATCAAAATTTCAAAGCA-AGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAG-AGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
16659 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
16703 GCTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
16747 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
16763 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
43 16 0.14
44 98 0.85
45 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:16739 original size:22 final size:22
Alignment explanation
Indices: 16494--16740 Score: 132
Period size: 22 Copynumber: 11.3 Consensus size: 22
16484 TAAAAGTCTC
*
16494 AATTTCATAAAGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
16514 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
16534 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
* *
16556 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATA-A-A-GAGGTTATCAA
* *
16581 AATTT-AT-AGGAAGCTTATCAA
1 AATTTCATAAAG-AGGTTATCAA
** **
16602 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
16624 AATTTC--AAAGCAAGGTTATCAA
1 AATTTCATAAAG--AGGTTATCAA
* * * * *
16646 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
* * * *
16668 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
* *
16690 AATTTTATAAAGAGCTTATCAA
1 AATTTCATAAAGAGGTTATCAA
16712 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
16734 ATTTTCA
1 AATTTCA
16741 AAATGTGATT
Statistics
Matches: 167, Mismatches: 46, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.01
20 22 0.13
21 23 0.14
22 101 0.60
23 1 0.01
24 6 0.04
25 13 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:16913 original size:22 final size:21
Alignment explanation
Indices: 16845--17324 Score: 146
Period size: 22 Copynumber: 22.0 Consensus size: 21
16835 ATATGGAGTA
** *
16845 ATCAAAATTTCAGGGA-GGAT
1 ATCAAAATTTCATAGAGGGTT
***
16865 ATCAAAATTTCATAGTTTAGTT
1 ATCAAAATTTCATAG-AGGGTT
*
16887 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCAT-AGAGGGTT
* *
16909 ATCAAAATTTCATAGTA-TGTAG
1 ATCAAAATTTCATAG-AGGGT-T
*
16931 ATCAAAATTTCATAGAGAGATT
1 ATCAAAATTTCATAGAG-GGTT
*
16953 AACAAAATTTCATA-ATGAGGTT
1 ATCAAAATTTCATAGA-G-GGTT
** * *
16975 ATCAAAAAATCATAGGGAGGCT
1 ATCAAAATTTCATAGAG-GGTT
*
16997 ATCAAAATTT-GT--A--GTT
1 ATCAAAATTTCATAGAGGGTT
* **
17013 ATCAATATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGAGGGTT
* *
17035 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA--GAGGGTT
* **
17058 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATA-G-AGGGTT
*
17081 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
* * *
17103 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGAG-GGTT
* * *
17125 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGAG-GGTT
17147 A-CTAACAA-TTCATATGTA-GGTT
1 ATC-AA-AATTTCATA-G-AGGGTT
* * *
17169 TTTAAATTTTCATA-ACGTGGTT
1 ATCAAAATTTCATAGA-G-GGTT
* *
17191 ATCAATATATCATATG-GAGGTT
1 ATCAAAATTTCATA-GAG-GGTT
* * *
17213 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGAG--GGTT
*
17236 ATCAAAATTTCATTG-GGAAGTT
1 ATCAAAATTTCATAGAGG--GTT
17258 ATCAAAATTTCATATTGA-GGTCT
1 ATCAAAATTTCATA--GAGGGT-T
* * *
17281 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGAG-GGTT
* *
17302 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT-AGAGGGTT
17324 A
1 A
17325 AAAAAAATTA
Statistics
Matches: 346, Mismatches: 72, Indels: 82
0.69 0.14 0.16
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
19 1 0.00
20 16 0.05
21 13 0.04
22 241 0.70
23 61 0.18
24 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATAGAGGGTT
Found at i:17001 original size:66 final size:62
Alignment explanation
Indices: 16845--17315 Score: 226
Period size: 66 Copynumber: 7.2 Consensus size: 62
16835 ATATGGAGTA
* *
16845 ATCAAAATTTC--AGGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGAGGGT
1 ATCAAAATTTCATAGGGAGG-TATCAAAATTTCATAG--GAGTTATCAAAATTTCATAAGA-GGT
16908 T
62 T
* * *
16909 ATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGAGAGATTAACAAAATTTCATAATGAGG
1 ATCAAAATTTCATAGGGAGGT--ATCAAAATTTCATAG-GAG-TTATCAAAATTTCATAA-GAGG
16973 TT
61 TT
** * * *
16975 ATCAAAAAATCATAGGGAGGCTATCAAAA-TT--T-GTAGTTATCAATATTTCATAAGAAAGTT
1 ATCAAAATTTCATAGGGAGG-TATCAAAATTTCATAGGAGTTATCAAAATTTCATAAG-AGGTT
* * *
17035 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAG
1 ATCAAAATTTCATAGGGAGG--TATCAAAATTTCATAGG-AG--TTATCAAAATTTCATA-AGAG
17100 GTT
60 GTT
* * * * *
17103 ATCACAATTTCATAGTGTGA-TTATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATGTA
1 ATCAAAATTTCATAG-G-GAGGTATCAAAATTTCATAG-GAG-TTATC-AA-AATTTCATAAG-A
17165 GGTT
59 GGTT
* * * ** * * * * * * *
17169 TTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGG
1 ATCAAAATTTCATAGGGAGG-TATCAAAATTTCATA-GGA-GTTATCAAAATTTCATA-AG-AGG
17234 TT
61 TT
* * * * * *
17236 ATCAAAATTTCATTGGGAAGTTATCAAAATTTCATATTGAGGTCT-TCAAAATTCCTTAGGGAGG
1 ATCAAAATTTCATAGGG-AGGTATCAAAATTTCATA-GGA-GT-TATCAAAATTTCATA-AGAGG
17300 TT
61 TT
*
17302 AACAAAATTTCATA
1 ATCAAAATTTCATA
17316 AGAAGGTTAA
Statistics
Matches: 310, Mismatches: 64, Indels: 64
0.71 0.15 0.15
Matches are distributed among these distances:
59 1 0.00
60 36 0.12
61 10 0.03
62 3 0.01
63 1 0.00
64 14 0.05
65 11 0.04
66 121 0.39
67 73 0.24
68 36 0.12
69 2 0.01
70 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (62 bp):
ATCAAAATTTCATAGGGAGGTATCAAAATTTCATAGGAGTTATCAAAATTTCATAAGAGGTT
Found at i:17105 original size:45 final size:44
Alignment explanation
Indices: 16845--17315 Score: 213
Period size: 44 Copynumber: 10.8 Consensus size: 44
16835 ATATGGAGTA
* * **
16845 ATCAAAATTTCA-GGGAGGA-TATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAGGAAGATTATCAAAATTTCATAG-CGAGGTT
* * * * * * *
16887 TTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAG-TATGTAG
1 ATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGT-T
* **
16931 ATCAAAATTTCATA-GAGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGA-AGATTATCAAAATTTCATAGCGAGGTT
** * ** *
16975 ATCAAAAAATCATAGGGAGGCTATCAAAA-TT--T-G-TA-GTT
1 ATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGTT
* * * *
17013 ATCAATATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGG-TT
*
17058 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGTT
* * * * * *
17103 ATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAAGATTATCAAAATTTCATAGCGAGGTT
* * * * * * * *
17147 A-CTAACAA-TTCATATGTAGGTTTTTAAATTTTCATAACGTGGTT
1 ATC-AA-AATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGTT
* * * * * * *
17191 ATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-GGAAGATTATCAAAATTTCATAGCG-AGGTT
* **
17236 ATCAAAATTTCATTGGGAAG-TTATCAAAATTTCATATTGAGGTCT
1 ATCAAAATTTCA-TAGGAAGATTATCAAAATTTCATAGCGAGGT-T
* * * * *
17281 -TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA
1 ATCAAAATTTCATAGGAAGATTATCAAAATTTCATA
17316 AGAAGGTTAA
Statistics
Matches: 326, Mismatches: 75, Indels: 54
0.72 0.16 0.12
Matches are distributed among these distances:
38 24 0.07
39 3 0.01
41 2 0.01
42 14 0.04
43 19 0.06
44 163 0.50
45 76 0.23
46 25 0.08
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGTT
Found at i:17337 original size:21 final size:22
Alignment explanation
Indices: 17297--17342 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17287 TTCCTTAGGG
* * *
17297 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAAA
17319 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTAAAAAAAATTCATAAAA
17340 AGG
1 AGG
17343 ATATCGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAAA
Found at i:18057 original size:12 final size:13
Alignment explanation
Indices: 18025--18058 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
18015 TCTGAAAATG
18025 ATATTATATATAT
1 ATATTATATATAT
18038 ATACTTATATATAT
1 ATA-TTATATATAT
18052 -TATTATA
1 ATATTATA
18059 AAAAACAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 5 0.25
14 10 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATTATATATAT
Done.