Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017628.1 Corchorus olitorius cultivar O-4 contig17661, 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: 56765
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:337 original size:34 final size:34
Alignment explanation
Indices: 294--359 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
284 GCAATTTAAA
294 GAGACTATGTAAGACAACTAAAAGGGAAAATATT
1 GAGACTATGTAAGACAACTAAAAGGGAAAATATT
* *
328 GAGACTATGTTAGACAATTAAAAGGGAAAATA
1 GAGACTATGTAAGACAACTAAAAGGGAAAATA
360 CTTTTGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (34 bp):
GAGACTATGTAAGACAACTAAAAGGGAAAATATT
Found at i:7695 original size:22 final size:22
Alignment explanation
Indices: 7670--7879 Score: 187
Period size: 22 Copynumber: 9.5 Consensus size: 22
7660 CTTGTCTGTG
*
7670 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
7692 TGGTTATTATAATTTTATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
7715 -GGTTATCAAATTTTGATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
7736 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
7759 -AGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
7780 AGGTTATCAAAATTTTATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
7802 TGG-TATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
7823 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* ** *
7847 AGGTTATTGAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGA
7869 TGGTTATCAAA
1 TGGTTATCAAA
7880 GAGATTATCA
Statistics
Matches: 151, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.01
21 21 0.14
22 106 0.70
23 7 0.05
24 16 0.11
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:7722 original size:44 final size:43
Alignment explanation
Indices: 7671--8587 Score: 191
Period size: 44 Copynumber: 21.4 Consensus size: 43
7661 TTGTCTGTGT
* *
7671 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTTATGAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTTAT-AGGA
* * * * *
7715 GGTTATCAAATTTTGAT-AGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTTATA-GGA
* * * *
7759 AGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTTATAG-GA
* *
7803 GG-TATCAAAATTTCATAGGATCAGGTTATTAAAATTTCT-TAGGAA
1 GGTTATCAAAATTTCATAAGAT--GGTTATCAAAATTT-TATAGG-A
**
7848 GGTTATTGAAATTTCAT-AGTATGGTTATC---A----A-A-GA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTTATAGGA
* * * * * *
7882 GATTATCAAAATGTCGTAGCGA-GGTTAT-AAGAATTTCATA--T
1 GGTTATCAAAATTTCATA-AGATGGTTATCAA-AATTTTATAGGA
* * * *
7923 GGTTAACAAAATTTCATAAGGA-GGTTA-CTAATATTTCATTGGGA
1 GGTTATCAAAATTTCATAA-GATGGTTATC-AAAATTTTA-TAGGA
* *
7967 GGTTATCAAAATTTCATATGAAGGTTAT-AAAAGTCTCAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAA---T---TTT-AT-AGGA
* * ** * * *
8017 -G-TACCAAAATTTGAT-AGAAAGTTATC-AAATCTCATAGAGT
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTTATAG-GA
** * *
8057 GGTTATTGAAATTTCACAAAGATCGGATTATCAAAATTTCATA-GA
1 GGTTATCAAAATTTCA-TAAGAT-GG-TTATCAAAATTTTATAGGA
** * *
8102 GTTGTTATCAAAATTTCA-AAGCGA-GGTTATCAAAATTACATAATGT
1 G--GTTATCAAAATTTCATAA--GATGGTTATCAAAATTTTAT-AGGA
* * * *
8148 GATTATCAAAATTTCAT-AGAGGGGTCAACAAAATTTTATAGAGA
1 GGTTATCAAAATTTCATAAGA-TGGTTATCAAAATTTTATAG-GA
* * * *
8192 GGTTATCAAAATTTCATAA-AGGGGTTATC-AAATTTTCAAAATGT
1 GGTTATCAAAATTTCATAAGA-TGGTTATCAAAATTTT--ATAGGA
* * * **
8236 GATTACCAAAATTTCAT-AG-TGG-TAT-----TTCTGGA-GA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTTATAGGA
*
8270 GGTTATCAAAATTTCAT-AGTATGGTTA-CCAAA---T-TAGGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTTATAGG-A
* * ** * * *
8309 GGTTATTAAACTTT--TATTATGGAGTAATCAAAATTTCA-GGGA
1 GGTTATCAAAATTTCATAAGAT-G-GTTATCAAAATTTTATAGGA
* * * * * *
8351 GGATATCAAAATTTCAT-AGTTTAGTTTTCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTTATAGGA
* *
8394 GGGTTATCAAAATTTCAT-AGTAT-GTAGATCAAAATTTCATAGGAAGA
1 -GGTTATCAAAATTTCATAAG-ATGGT-TATCAAAATTTTATA-G--GA
* * ** * *
8441 GGTTATCAAAATTT-GT-TG-TAATTATCAAGATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTTAT-AGGA
* * *
8482 GGCTATCAAAATTTTATAGGGA-GGTTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATA-AGATGG-TTATCAAAATTTTATAGG-A
* * * *
8527 GGTTTATCAAAATTTCATAACGA-GGTTATTACAATTTCATAGTGT
1 GG-TTATCAAAATTTCATAA-GATGGTTATCAAAATTTTATAG-GA
*
8572 GATTATCAAAATTTCA
1 GGTTATCAAAATTTCA
8588 GAGGTGATTA
Statistics
Matches: 643, Mismatches: 131, Indels: 198
0.66 0.13 0.20
Matches are distributed among these distances:
34 37 0.06
35 3 0.00
36 5 0.01
37 10 0.02
38 3 0.00
39 18 0.03
40 7 0.01
41 49 0.08
42 43 0.07
43 56 0.09
44 235 0.37
45 64 0.10
46 56 0.09
47 37 0.06
48 12 0.02
49 4 0.01
50 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTTATAGGA
Found at i:7749 original size:66 final size:66
Alignment explanation
Indices: 7667--7879 Score: 254
Period size: 66 Copynumber: 3.2 Consensus size: 66
7657 TTTCTTGTCT
* * *
7667 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTTATGAGG-AGGTTATC-AAATTTTG
1 GTGTGGTTATCAAAATTTCATAGGATGGTTATTAAAATTTCAT-AGGAAGGTTATCAAAATTTT-
7730 ATA
64 ATA
* * *
7733 GTGTGGTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTTA
1 GTGTGGTTATCAAAATTTCATA-GGATGGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTTA
7797 TA
65 TA
* ** *
7799 GTGTGG-TATCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTATCAAAATTTCATAGGAT--GGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTT
7863 ATA
64 ATA
*
7866 GTATGGTTATCAAA
1 GTGTGGTTATCAAA
7880 GAGATTATCA
Statistics
Matches: 126, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
64 3 0.02
65 17 0.13
66 51 0.40
67 48 0.38
68 7 0.06
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (66 bp):
GTGTGGTTATCAAAATTTCATAGGATGGTTATTAAAATTTCATAGGAAGGTTATCAAAATTTTAT
A
Found at i:7958 original size:22 final size:22
Alignment explanation
Indices: 7923--8253 Score: 155
Period size: 22 Copynumber: 14.8 Consensus size: 22
7913 AATTTCATAT
*
7923 GGTTAACAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGGA
* **
7945 GGTTA-CTAATATTTCATTGGGA
1 GGTTATC-AAAATTTCATAAGGA
* *
7967 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAAGGA
*
7989 GGTTATAAAAGTCTCAATTTCATAAGGA
1 GGTTAT-CAA-----AATTTCATAAGGA
* * *
8017 -G-TACCAAAATTTGAT-AGAA
1 GGTTATCAAAATTTCATAAGGA
* * *
8036 AGTTATC-AAATCTCAT-AGAGT
1 GGTTATCAAAATTTCATAAG-GA
** * *
8057 GGTTATTGAAATTTCACAAAGA
1 GGTTATCAAAATTTCATAAGGA
8079 TCGGATTATCAAAATTTCAT-A-GA
1 --GG-TTATCAAAATTTCATAAGGA
8102 GTTGTTATCAAAATTTCA-AAGCGA
1 G--GTTATCAAAATTTCATAAG-GA
* * *
8126 GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAAGGA
*
8148 GATTATCAAAATTTCATAGAGG-
1 GGTTATCAAAATTTCATA-AGGA
* * *
8170 GGTCAACAAAATTTTAT-AGAGA
1 GGTTATCAAAATTTCATAAG-GA
8192 GGTTATCAAAATTTCATAAAGG-
1 GGTTATCAAAATTTCAT-AAGGA
* * * *
8214 GGTTATCAAATTTTCAAAATGT
1 GGTTATCAAAATTTCATAAGGA
* *
8236 GATTACCAAAATTTCATA
1 GGTTATCAAAATTTCATA
8254 GTGGTATTTC
Statistics
Matches: 233, Mismatches: 48, Indels: 56
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.01
20 19 0.08
21 14 0.06
22 149 0.64
23 12 0.05
24 8 0.03
25 14 0.06
26 2 0.01
27 1 0.00
28 11 0.05
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGGA
Found at i:8160 original size:66 final size:66
Alignment explanation
Indices: 8081--8229 Score: 190
Period size: 66 Copynumber: 2.3 Consensus size: 66
8071 CACAAAGATC
** * * * *
8081 GGATTATCAAAATTTCATAGAGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAAT
1 GGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
8146 G
66 G
* * * *
8147 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAA
1 GGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
8212 G
66 G
* *
8213 GGGTTATCAAATTTTCA
1 GGATTATCAAAATTTCA
8230 AAATGTGATT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (66 bp):
GGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAAA
G
Found at i:8477 original size:65 final size:64
Alignment explanation
Indices: 8421--8585 Score: 156
Period size: 68 Copynumber: 2.5 Consensus size: 64
8411 TAGTATGTAG
*
8421 ATCAAAATTTCATAGGAAGAGG-TTATCAAAATTTGTTGTAATTATCAAGATTTCATAAGGAGGC
1 ATCAAAATTTCATAGG--GAGGTTTATCAAAATTTGTTGTAATTATCAAAATTTCATAAGGAGGC
8485 T
64 T
* * *
8486 ATCAAAATTTTATAGGGAGGTTTATCAAAATTT-TATAGGAAGGTTTATCAAAATTTCATAACGA
1 ATCAAAATTTCATAGGGAGGTTTATCAAAATTTGT-T-GTAA---TTATCAAAATTTCATAAGGA
*
8550 GGTT
61 GGCT
* * * * *
8554 ATTACAATTTCATAGTG-TGATTATCAAAATTT
1 ATCAAAATTTCATAGGGAGGTTTATCAAAATTT
8586 CAGAGGTGAT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
63 5 0.06
64 13 0.16
65 18 0.22
67 13 0.16
68 34 0.41
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (64 bp):
ATCAAAATTTCATAGGGAGGTTTATCAAAATTTGTTGTAATTATCAAAATTTCATAAGGAGGCT
Found at i:8489 original size:87 final size:87
Alignment explanation
Indices: 8378--8541 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 87
8368 AGTTTAGTTT
* * *
8378 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTCATAGGAAGAG
1 TCAAAATTTCATAAGAGGGCTATCAAAATTTCATAGGGAGGTAGATCAAAATTTCATAGGAAG-G
8442 GTTATCAAAATTTGTTGTAATTA
65 GTTATCAAAATTTGTTGTAATTA
* * ** *
8465 TCAAGATTTCATAAG-GAGGCTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGG
1 TCAAAATTTCATAAGAG-GGCTATCAAAATTTCATAGGGAGGTAGATCAAAATTTCATAGGAAGG
*
8529 TTTATCAAAATTT
65 GTTATCAAAATTT
8542 CATAACGAGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.02
87 43 0.65
88 22 0.33
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (87 bp):
TCAAAATTTCATAAGAGGGCTATCAAAATTTCATAGGGAGGTAGATCAAAATTTCATAGGAAGGG
TTATCAAAATTTGTTGTAATTA
Found at i:8515 original size:23 final size:23
Alignment explanation
Indices: 8462--8541 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
8452 TTTGTTGTAA
* * *
8462 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
8484 CTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
8507 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
8530 TTATCAAAATTT
1 TTATCAAAATTT
8542 CATAACGAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 18 0.35
23 33 0.65
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Found at i:8552 original size:23 final size:22
Alignment explanation
Indices: 8335--8587 Score: 141
Period size: 22 Copynumber: 11.5 Consensus size: 22
8325 TTATGGAGTA
* *
8335 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
*
8355 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
*
8377 TTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * *
8399 ATCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
*
8421 ATCAAAATTTCATAGGAAGAGGTT
1 ATCAAAATTTCATA--AGGAGGTT
* * * *
8445 ATCAAAATTT-GT-TGTA-ATT
1 ATCAAAATTTCATAAGGAGGTT
* *
8464 ATCAAGATTTCATAAGGAGGCT
1 ATCAAAATTTCATAAGGAGGTT
* *
8486 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
*
8509 ATCAAAATTTTAT-AGGAAGGTTT
1 ATCAAAATTTCATAAGG-AGG-TT
*
8532 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
8554 ATTACAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
8576 ATCAAAATTTCA
1 ATCAAAATTTCA
8588 GAGGTGATTA
Statistics
Matches: 176, Mismatches: 38, Indels: 36
0.70 0.15 0.14
Matches are distributed among these distances:
19 11 0.06
20 14 0.08
21 7 0.04
22 90 0.51
23 38 0.22
24 12 0.07
25 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:8606 original size:22 final size:23
Alignment explanation
Indices: 8557--8606 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
8547 CGAGGTTATT
*
8557 ACAATTTCATAGTGTGATTATCA
1 ACAATTTCAGAGTGTGATTATCA
8580 A-AATTTCAGAG-GTGATTA-CTA
1 ACAATTTCAGAGTGTGATTATC-A
8601 ACAATT
1 ACAATT
8607 CATATGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 9 0.38
22 13 0.54
23 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (23 bp):
ACAATTTCAGAGTGTGATTATCA
Found at i:8697 original size:22 final size:22
Alignment explanation
Indices: 8658--8721 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
8648 AATCATTTTT
* * *
8658 AAGTTATCAACATCTCATAGAT
1 AAGTTATCAAAATTTCATAGAG
* * *
8680 TAGTTATCAAAATTTCATTGGG
1 AAGTTATCAAAATTTCATAGAG
*
8702 AAGTTATCGAAATTTCATAG
1 AAGTTATCAAAATTTCATAG
8722 TGAGATCTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (22 bp):
AAGTTATCAAAATTTCATAGAG
Found at i:8771 original size:22 final size:22
Alignment explanation
Indices: 8746--8787 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8736 TTCCTTAGGG
*
8746 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTT-ATAAGA
8768 AGGTTAAAAAAAATTTATAA
1 AGGTTAAAAAAAATTTATAA
8788 AAAGATCTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAGA
Found at i:8829 original size:22 final size:22
Alignment explanation
Indices: 8798--8851 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
8788 AAAGATCTCG
* * * *
8798 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGAAACGTTATCA
*
8820 AAATTTCATAGAAAGGTTATCA
1 AAATTTCATAGAAACGTTATCA
8842 AAATTTCATA
1 AAATTTCATA
8852 AGGAGGTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGAAACGTTATCA
Found at i:8863 original size:22 final size:22
Alignment explanation
Indices: 8819--8866 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
8809 TATCGTTATT
*
8819 AAAATTTCATAGAAAGGTTATC
1 AAAATTTCATAGAAAGGTAATC
*
8841 AAAATTTCATA-AGGAGGTAATC
1 AAAATTTCATAGA-AAGGTAATC
8863 AAAA
1 AAAA
8867 ATAGCGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGAAAGGTAATC
Found at i:11921 original size:22 final size:20
Alignment explanation
Indices: 11871--11922 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
11861 TAGTGAGTTT
11871 TATTATTATTATTATAAAATA
1 TATTA-TATTATTATAAAATA
* *
11892 -ATTCTATTATATATATATATA
1 TATTATATTAT-TATA-AAATA
11913 TATTATATTA
1 TATTATATTA
11923 CTAATTGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 6 0.24
20 7 0.28
21 4 0.16
22 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTATATTATTATAAAATA
Found at i:12045 original size:113 final size:113
Alignment explanation
Indices: 11916--12136 Score: 354
Period size: 113 Copynumber: 2.0 Consensus size: 113
11906 ATATATATAT
*
11916 TATATTACTAATTGTGTGGTTTATTCAATTGAA-TCTATTAAATAAGCACACATACCAAACAATA
1 TATATTACTAATTGTGTGGTTTATTCAATTAAACT-TATTAAATAAGCACACATACCAAACAATA
* *
11980 CAAAATGCAATAAATTATTGGATTTAAAGAAAAATACAAGCACCTATTA
65 CAAAATGCAACAAACTATTGGATTTAAAGAAAAATACAAGCACCTATTA
* * *
12029 TATATTATTAATTGTGTTGTTTATTCAATTAAACTTATTAAATAAGCACACATACCATACAATAC
1 TATATTACTAATTGTGTGGTTTATTCAATTAAACTTATTAAATAAGCACACATACCAAACAATAC
* *
12094 AAAGTGCAACGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 AAAATGCAACAAACTATTGGATTTAAAGAAAAATACAAGCACC
12137 AAAATGACTA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 98 0.99
114 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (113 bp):
TATATTACTAATTGTGTGGTTTATTCAATTAAACTTATTAAATAAGCACACATACCAAACAATAC
AAAATGCAACAAACTATTGGATTTAAAGAAAAATACAAGCACCTATTA
Found at i:12311 original size:16 final size:16
Alignment explanation
Indices: 12290--12322 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12280 AAAATATAAT
12290 TACTTTCTTGAGCAAA
1 TACTTTCTTGAGCAAA
12306 TACTTTCTTGAGCAAA
1 TACTTTCTTGAGCAAA
12322 T
1 T
12323 TTTCTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (16 bp):
TACTTTCTTGAGCAAA
Found at i:13121 original size:2 final size:2
Alignment explanation
Indices: 13114--13172 Score: 54
Period size: 2 Copynumber: 29.5 Consensus size: 2
13104 ACTCAAATAA
13114 AT AT AT AT AT AT AT AT AT AT AT ACT A- AT ACT A- AT ACT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT
13154 ACT A- AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT A
13173 AATTAAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
1 4 0.08
2 37 0.76
3 8 0.16
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:13184 original size:42 final size:44
Alignment explanation
Indices: 13113--13228 Score: 141
Period size: 45 Copynumber: 2.7 Consensus size: 44
13103 AACTCAAATA
* * * * *
13113 AATATATATATATATATATATATACTAATACTAATACTAATACT
1 AATATATATATATATAAATATATAATAATAATAATAATAATAAT
*
13157 AATATATATATATATAAATTAAATAATAATAATAATAATAATAAT
1 AATATATATATATATAAA-TATATAATAATAATAATAATAATAAT
13202 AATA-ATATA-ATAT-AATA-ATAATAATAA
1 AATATATATATATATAAATATATAATAATAA
13229 ATATTATTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 10 0.15
41 2 0.03
42 2 0.03
43 4 0.06
44 22 0.34
45 25 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (44 bp):
AATATATATATATATAAATATATAATAATAATAATAATAATAAT
Found at i:13186 original size:3 final size:3
Alignment explanation
Indices: 13178--13228 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
13168 ATATAAATTA
13178 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13224 AAT AA
1 AAT AA
13229 ATATTATTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:13187 original size:6 final size:6
Alignment explanation
Indices: 13138--13228 Score: 89
Period size: 6 Copynumber: 15.0 Consensus size: 6
13128 ATATATATAC
* * * *
13138 TAATAC TAATAC TAATAC TAATATA TATATATA TAA-AT TAAATAA TAATAA
1 TAATAA TAATAA TAATAA TAATA-A TA-ATA-A TAATAA T-AATAA TAATAA
13189 TAATAA TAATAA TAATAA T-ATAA T-ATAA TAATAA TAATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
13229 ATATTATTTG
Statistics
Matches: 77, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
5 11 0.14
6 54 0.70
7 5 0.06
8 7 0.09
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (6 bp):
TAATAA
Found at i:17071 original size:27 final size:27
Alignment explanation
Indices: 17030--17083 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
17020 CTCATTATAG
* *
17030 GGGGTAAAATCGTAATTTTATCAATCA
1 GGGGTAAAATAGTAAATTTATCAATCA
* *
17057 GGGGTAATATAGTAAATTTATCCATCA
1 GGGGTAAAATAGTAAATTTATCAATCA
17084 CGGATATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (27 bp):
GGGGTAAAATAGTAAATTTATCAATCA
Found at i:32934 original size:21 final size:21
Alignment explanation
Indices: 32867--32935 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
32857 ATCATGCCCG
*
32867 GCCAAGACCGGCCACAGCCAT
1 GCCAAGACCGGCCACAACCAT
**
32888 GCCATTACCGGCCATC-ACCGA-
1 GCCAAGACCGGCCA-CAACC-AT
32909 GCCAAGACCGGCCACAACCAT
1 GCCAAGACCGGCCACAACCAT
*
32930 CCCAAG
1 GCCAAG
32936 GCGAGCCTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.05
21 34 0.89
22 2 0.05
ACGTcount: A:0.29, C:0.43, G:0.20, T:0.07
Consensus pattern (21 bp):
GCCAAGACCGGCCACAACCAT
Found at i:33470 original size:20 final size:21
Alignment explanation
Indices: 33428--33471 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
33418 TTTCCTTTGC
* *
33428 ATTGTTTTGTCTTGATTGGTT
1 ATTGCTTTGTCTTGATTGCTT
*
33449 ATTGCTTTG-CTTGCTTGCTT
1 ATTGCTTTGTCTTGATTGCTT
33469 ATT
1 ATT
33472 CCTTGATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.59
Consensus pattern (21 bp):
ATTGCTTTGTCTTGATTGCTT
Found at i:34303 original size:21 final size:21
Alignment explanation
Indices: 34274--34315 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
34264 TCGCTCGGTC
*
34274 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
34294 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
34316 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:35173 original size:25 final size:25
Alignment explanation
Indices: 35135--35183 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
35125 CCAAACAATC
*
35135 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTATCGCTCGGTCTCTAT
35160 TTGAGCACTATCGCTCGGTCTCTA
1 TTGAGCACTATCGCTCGGTCTCTA
35184 CAAACCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.31, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTATCGCTCGGTCTCTAT
Found at i:35209 original size:21 final size:21
Alignment explanation
Indices: 35180--35222 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35170 TCGCTCGGTC
*
35180 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
35200 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
35222 T
1 T
35223 ACACACACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.19
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:36412 original size:29 final size:26
Alignment explanation
Indices: 36379--36448 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 26
36369 GTGGATTGTA
*
36379 AAAATAAAATTGAATAATTTAAGAACATT
1 AAAATAAAATTGAAGAA-TT-A-AACATT
* *
36408 AAAATAAATTTTAAGAATTAAACATT
1 AAAATAAAATTGAAGAATTAAACATT
*
36434 AAAA-AAAATTCAAGA
1 AAAATAAAATTGAAGA
36449 CTGACCCAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 9 0.25
26 10 0.28
27 1 0.03
28 2 0.06
29 14 0.39
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (26 bp):
AAAATAAAATTGAAGAATTAAACATT
Found at i:39109 original size:36 final size:36
Alignment explanation
Indices: 39069--39140 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
39059 AGTGGAGAGG
*
39069 AGCCAGATCCTCTTAAACACCCAAGCCTTGTATTTA
1 AGCCAAATCCTCTTAAACACCCAAGCCTTGTATTTA
*
39105 AGCCAAATCCTCTTAAACACTCAAGCCTTGTATTTA
1 AGCCAAATCCTCTTAAACACCCAAGCCTTGTATTTA
39141 TATACTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (36 bp):
AGCCAAATCCTCTTAAACACCCAAGCCTTGTATTTA
Found at i:42505 original size:30 final size:30
Alignment explanation
Indices: 42471--42546 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
42461 GTAGAGTAAT
42471 CAAGCCTTAAATTG-AAGCAAATCAA-CATAA
1 CAAGCCTTAAATTGCAA-C-AATCAATCATAA
* * *
42501 CAAGCCTCAAATTGCAACAATTAATCATGA
1 CAAGCCTTAAATTGCAACAATCAATCATAA
*
42531 CAAGTCTTAAATTGCA
1 CAAGCCTTAAATTGCA
42547 GTAATCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 5 0.13
30 32 0.82
31 2 0.05
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (30 bp):
CAAGCCTTAAATTGCAACAATCAATCATAA
Found at i:47980 original size:21 final size:21
Alignment explanation
Indices: 47956--48004 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
47946 CTAAGATGCA
*
47956 TAAAAA-AATAAATCTTAAATC
1 TAAAAACAAGAAA-CTTAAATC
47977 TAAAAACAAGAAACTTAAAT-
1 TAAAAACAAGAAACTTAAATC
47997 TGAAAAAC
1 T-AAAAAC
48005 CCTAAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.63, C:0.10, G:0.04, T:0.22
Consensus pattern (21 bp):
TAAAAACAAGAAACTTAAATC
Done.