Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013616.1 Corchorus olitorius cultivar O-4 contig13649, 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: 25968
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36 CTATTCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40 original size:8 final size:7
Alignment explanation
Indices: 1--52 Score: 50
Period size: 8 Copynumber: 6.7 Consensus size: 7
1 TATATAT
1 TATATAT
8 ATATATAT
1 -TATATAT
16 ATATATAT
1 -TATATAT
24 ATATATAT
1 -TATATAT
32 TATACTAT
1 TATA-TAT
*
40 TCTTATAT
1 T-ATATAT
48 TATAT
1 TATAT
53 GGAATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 7 0.17
8 31 0.77
9 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:199 original size:6 final size:6
Alignment explanation
Indices: 188--219 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
178 TTACCGGATG
188 TATGTA TATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TA
220 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:306 original size:2 final size:2
Alignment explanation
Indices: 301--329 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
291 TTTTTTACTA
301 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
330 TGCTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:319 original size:15 final size:15
Alignment explanation
Indices: 299--329 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
289 CTTTTTTTAC
299 TAATATATATATATA
1 TAATATATATATATA
314 TAATATATATATATA
1 TAATATATATATATA
329 T
1 T
330 TGCTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:321 original size:13 final size:13
Alignment explanation
Indices: 303--328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
293 TTTTACTAAT
303 ATATATATATATA
1 ATATATATATATA
316 ATATATATATATA
1 ATATATATATATA
329 TTGCTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1576 original size:44 final size:45
Alignment explanation
Indices: 1477--2543 Score: 414
Period size: 44 Copynumber: 24.9 Consensus size: 45
1467 GTCTCTGTGT
** * * *
1477 GGTTATCAAAATTTCATA-AAATAGTTATTATAATTTCAT--G-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* *
1518 GGTCATCAAAATTTCATAGTG-TGGTTACCAAAATTTCATATGGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATA-GGAA
* * * *
1563 -GTTATCAAAATTTCAT-GGGAAGGTTATCAAAATGTCATAGTG-T
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GAA
* * **
1606 GGTTACCAAAATTTCATAG-GATCAGGTTATTAAAATTTTTTAGGAA
1 GGTTATCAAAATTTCATAGTGAT--GGTTATCAAAATTTCATAGGAA
** * * *
1652 GGTTATTGAAATTTCATAGTG-TGGTTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* *
1696 GGTTATC---A----A-A--GA-GATTATCAAAATGTCATAGCG-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GAA
* * *
1730 GGTTAT-AAGAATTTCATAGTG-TGGTTAACAAAATTTCATAGTAT
1 GGTTATCAA-AATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* * *
1774 GGTTAACAAAATTTCATAAG-GA-GGTTA-CTAATATTTCATAGGGA
1 GGTTATCAAAATTTCAT-AGTGATGGTTATC-AAAATTTCATAGGAA
* * * *
1818 GGTTATCAAAATTTCATAGT-TTGGTTATTAAAATGTT-TTAGTG-T
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAAT-TTCATAG-GAA
* *
1862 GGTTATCAAAATTTCATA-TGACGGTTATAAAAGTCTCAATTTCATAGGAA
1 GGTTATCAAAATTTCATAGTGATGGTTAT-CAA-----AATTTCATAGGAA
* * * * *
1912 --ATACCAAAATTTGATA--GAAGGTTATC-AAATCTCATA-G-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* *
1950 GTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTT-ATAGGAA
1 G-G-TTATCAAAATTTCATAGTGAT-GG-TTATCAAAATTTCATAGGAA
* * *
1998 GATTATCAAAATTTCATAGTG-TTGTTATCAAAATTTCAAAGCG-A
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GAA
* * *** *
2042 GGTTATCAAAATTACATAATGA-AAATATCAAAATTTCATA-GAG
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* * * * *
2085 GCGTCAACAAAATTTTATAGAGA-GGTTATCAAAATTTCATA-AAGA
1 G-GTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGA-A
* * * *
2130 GGTTATCAAATTTTCAAAATG-TGG---T----ATTTC-TGGGGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCAT-AGGAA
2167 -GTTATCAAAATTTCATAGT-ATGGTTATC-AAA--T--TAGGAA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* * * * *
2205 GGTTATTAAACTTT--TA-TCATGGAGTAATCAAAA-TTC--AGGGA
1 GGTTATCAAAATTTCATAGTGAT-G-GTTATCAAAATTTCATAGGAA
* * **
2246 GGATATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAGTTTA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAG-GAA
* * * *
2291 -GTTTTCAAAATTTCATA-AGAGGGTTATCAAAATTTCATA-GCA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* * * * * *
2333 TGTAGATCAAAATTTCATAGGGA-GATTAACAAAATTTCATAATG-A
1 GGT-TATCAAAATTTCATAGTGATGGTTATCAAAATTTCAT-AGGAA
** * *
2378 GGTTATCAAAAAATCATAGGGA-GGTTATCAAAA-TT--T--GTA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
* * *
2417 -GTTATCAAGATTTCATAAG-GA-GGTTATTAAAATTTTATAGGGAA
1 GGTTATCAAAATTTCAT-AGTGATGGTTATCAAAATTTCATA-GGAA
* * * *
2461 GTTTATCAAAATTTTATAG-GAAGGTTTATCAAAATTTCATAACG-A
1 GGTTATCAAAATTTCATAGTGATGG-TTATCAAAATTTCAT-AGGAA
* **
2506 GGTTATCACAATTTCATAGT-ATAATTATCAAAATTTCA
1 GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCA
2544 GTGTGTGATT
Statistics
Matches: 773, Mismatches: 149, Indels: 205
0.69 0.13 0.18
Matches are distributed among these distances:
34 23 0.03
36 22 0.03
37 12 0.02
38 33 0.04
39 24 0.03
40 12 0.02
41 61 0.08
42 20 0.03
43 28 0.04
44 368 0.48
45 58 0.08
46 72 0.09
47 16 0.02
48 15 0.02
49 3 0.00
50 6 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAGTGATGGTTATCAAAATTTCATAGGAA
Found at i:1669 original size:68 final size:65
Alignment explanation
Indices: 1473--2543 Score: 313
Period size: 66 Copynumber: 16.6 Consensus size: 65
1463 TCTTGTCTCT
* ** * * *
1473 GTGTGGTTATCAAAATTTCATAAAATAGTTATTATAATTTCAT--G-AGGTCATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAGGA-AGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
1535 A
65 A
* *
1536 GTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATTTCATGGGAAGGTTATCAAAATGTCAT
1 GTGTGGTTACCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
1601 A
65 A
* ** **
1602 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGA--A-GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTC
1667 ATA
63 ATA
* * * * * *
1670 GTGTGGTTATCACAATTTTATAGAAAGGTTATC---A----A-A-G-AGATTATCAAAATGTCAT
1 GTGTGGTTACCAAAATTTCATAGGAA-GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
1725 A
65 A
* * * ** * * * *
1726 GCGAGGTTA-TAAGAATTTCATAGTGTGGTTAACAAAATTTCATAGTATGGTTAACAAAATTTCA
1 GTGTGGTTACCAA-AATTTCATAG-GAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCA
1790 TAA
64 T-A
* * * * *** * *
1793 G-GAGGTTACTAATATTTCATAGGGAGGTTATCAAAATTTCATAGTTTGGTTATTAAAATGTT-T
1 GTGTGGTTACCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAAT-TTCA
1856 TA
64 TA
* * * * * *
1858 GTGTGGTTATCAAAATTTCATATGACGGTTATAAAAGTCTCAATTTCATAGGAA--ATACCAAAA
1 GTGTGGTTACCAAAATTTCATAGGA-AGTTAT-CAA-----AATTTCATAGGAAGGTTATCAAAA
*
1921 TTTGATA
59 TTTCATA
** * * * * *
1928 G-AAGGTTATC-AAATCTCATA-GAGTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATT
1 GTGTGGTTACCAAAATTTCATAGGA-AG-TTATCAAAATTTCATAG-GA-AGG-TTATCAAAATT
1990 T-ATA
61 TCATA
* * * ** * *
1994 G-GAAGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCG-AGGTTATCAAAATTAC
1 GTG-TGGTTACCAAAATTTCATAG-GAAGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTC
2057 ATA
63 ATA
* **** * ** * * *
2060 ATGAAAATATCAAAATTTCATAGAGGCGTCAACAAAATTTTATA-GAGAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAG-GAAGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCA
2124 TA
64 TA
** * * * ** *
2126 AAGAGGTTATCAAATTTTCA-A--AATGTGGT----ATTTC-TGGGGAA-GTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAGGAA-GTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCA
2182 TA
64 TA
* * * * * *
2184 GTATGGTTATC-AAA--T--TAGGAAGGTTATTAAACTTTTATCATGG-A-GTAATCAAAA-TTC
1 GTGTGGTTACCAAAATTTCATAGGAA-GTTATCAAAATTTCAT-A-GGAAGGTTATCAAAATTTC
2241 --A
63 ATA
* * * * * ** *
2242 GGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAGGAA-GTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCA
2306 TAA
64 T-A
* * * * * * * *
2309 GAG-GGTTATCAAAATTTCATAGCATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAGGAAGT-TATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
2373 A
65 A
* * * ** * * *
2374 ATGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T--GTA-GTTATCAAGATTTCAT
1 GTGTGGTTACCAAAATTTCATA-GGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
2433 AA
65 -A
* ** * *
2435 G-GAGGTTATTAAAATTTTATAGGGAAGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTC
1 GTGTGGTTACCAAAATTTCATA-GGAAG-TTATCAAAATTTCATAGGAAGG-TTATCAAAATTTC
2499 ATA
63 ATA
** * * * * *
2502 ACGAGGTTATCACAATTTCATAGTATAATTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAGGA-AGTTATCAAAATTTCA
2544 GTGTGTGATT
Statistics
Matches: 763, Mismatches: 161, Indels: 164
0.70 0.15 0.15
Matches are distributed among these distances:
54 1 0.00
55 2 0.00
56 41 0.05
57 3 0.00
58 34 0.04
59 9 0.01
60 42 0.06
61 25 0.03
62 15 0.02
63 71 0.09
64 7 0.01
65 27 0.04
66 274 0.36
67 57 0.07
68 123 0.16
69 11 0.01
70 11 0.01
72 10 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
Found at i:1677 original size:22 final size:22
Alignment explanation
Indices: 1473--1692 Score: 132
Period size: 22 Copynumber: 10.0 Consensus size: 22
1463 TCTTGTCTCT
1473 GTGTGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*** * * *
1495 AAATAGTTATTATAATTTC--A
1 GTGTGGTTATCAAAATTTCATA
* *
1515 -TGAGGTCATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
1536 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
1558 -TG-GAAGTTATCAAAATTTCAT-
1 GTGTG--GTTATCAAAATTTCATA
* * *
1579 GGGAAGGTTATCAAAATGTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
1602 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* **
1624 G-GATCAGGTTATTAAAATTTTTTA
1 GTG-T--GGTTATCAAAATTTCATA
* **
1648 G-GAAGGTTATTGAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
* *
1670 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
1692 G
1 G
1693 AAAGGTTATC
Statistics
Matches: 149, Mismatches: 36, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
19 11 0.07
20 2 0.01
21 4 0.03
22 111 0.74
23 3 0.02
24 18 0.12
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:1735 original size:22 final size:22
Alignment explanation
Indices: 1710--2145 Score: 250
Period size: 22 Copynumber: 19.6 Consensus size: 22
1700 ATCAAAGAGA
* *
1710 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
*
1732 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
1754 TTAACAAAATTTCATAGT-ATGG
1 TTATCAAAATTTCATAGTGA-GG
*
1776 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* *
1798 TTA-CTAATATTTCATAGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
**
1820 TTATCAAAATTTCATAGTTTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
1842 TTATTAAAATGTT-TTAGTGTGG
1 TTATCAAAAT-TTCATAGTGAGG
1864 TTATCAAAATTTCATA-TGACGG
1 TTATCAAAATTTCATAGTGA-GG
* *
1886 TTATAAAAGTCTCAATTTCATAG-GA-A
1 TTAT-CAA-----AATTTCATAGTGAGG
* * * *
1912 ATACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
1933 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
1954 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
1978 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
2000 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
2022 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * **
2044 TTATCAAAATTACATAATGAAA
1 TTATCAAAATTTCATAGTGAGG
* *
2066 ATATCAAAATTTCATAGAG-GCG
1 TTATCAAAATTTCATAGTGAG-G
* * * *
2088 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
2110 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
*
2132 TTATCAAATTTTCA
1 TTATCAAAATTTCA
2146 AAATGTGGTA
Statistics
Matches: 321, Mismatches: 64, Indels: 58
0.72 0.14 0.13
Matches are distributed among these distances:
20 19 0.06
21 30 0.09
22 227 0.71
23 13 0.04
24 6 0.02
25 13 0.04
26 2 0.01
28 11 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:2276 original size:41 final size:40
Alignment explanation
Indices: 2169--2280 Score: 104
Period size: 41 Copynumber: 2.8 Consensus size: 40
2159 CTGGGGAAGT
* *
2169 TATCAAAATTTCATA-GTATGGTTATC-AAATTAGGAAGGT
1 TATCAAAATTTCATATG-AAGGTTATCAAAATTAGGAAGGA
* * * * * *
2208 TATTAAACTTTTATCATGGA-GTAATCAAAATTCAGGGAGGA
1 TATCAAAATTTCAT-ATGAAGGTTATCAAAATT-AGGAAGGA
2249 TATCAAAATTTCATATGAAGGTTATCAAAATT
1 TATCAAAATTTCATATGAAGGTTATCAAAATT
2281 TCATAGTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
39 16 0.29
40 10 0.18
41 29 0.53
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (40 bp):
TATCAAAATTTCATATGAAGGTTATCAAAATTAGGAAGGA
Found at i:2277 original size:22 final size:22
Alignment explanation
Indices: 2163--2543 Score: 205
Period size: 22 Copynumber: 17.9 Consensus size: 22
2153 GTATTTCTGG
2163 GGAA-GTTATCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATA
* *
2184 GTATGGTTATC-AAA--T--TA
1 GGAAGGTTATCAAAATTTCATA
* * *
2201 GGAAGGTTATTAAACTTTTATCA
1 GGAAGGTTATCAAAATTTCAT-A
*
2224 TGG-A-GTAATCAAAA-TTC--A
1 -GGAAGGTTATCAAAATTTCATA
* *
2242 GGGAGGATATCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATA
*
2264 TGAAGGTTATCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATA
** *
2286 GTTTA-GTTTTCAAAATTTCATA
1 G-GAAGGTTATCAAAATTTCATA
* *
2308 AGAGGGTTATCAAAATTTCATA
1 GGAAGGTTATCAAAATTTCATA
* * *
2330 -GCATGTAGATCAAAATTTCATA
1 GGAAGGT-TATCAAAATTTCATA
* * *
2352 GGGAGATTAACAAAATTTCATAA
1 GGAAGGTTATCAAAATTTCAT-A
* **
2375 TG-AGGTTATCAAAAAATCATA
1 GGAAGGTTATCAAAATTTCATA
*
2396 GGGAGGTTATCAAAA-TT--T-
1 GGAAGGTTATCAAAATTTCATA
* *
2414 -GTA-GTTATCAAGATTTCATAA
1 GGAAGGTTATCAAAATTTCAT-A
* *
2435 GG-AGGTTATTAAAATTTTATA
1 GGAAGGTTATCAAAATTTCATA
* *
2456 GGGAAGTTTATCAAAATTTTATA
1 -GGAAGGTTATCAAAATTTCATA
2479 GGAAGGTTTATCAAAATTTCATAA
1 GGAAGG-TTATCAAAATTTCAT-A
* *
2503 CG-AGGTTATCACAATTTCATA
1 GGAAGGTTATCAAAATTTCATA
* *
2524 GTATA-ATTATCAAAATTTCA
1 GGA-AGGTTATCAAAATTTCA
2544 GTGTGTGATT
Statistics
Matches: 273, Mismatches: 55, Indels: 63
0.70 0.14 0.16
Matches are distributed among these distances:
16 9 0.03
17 16 0.06
18 4 0.01
19 11 0.04
20 4 0.01
21 16 0.06
22 166 0.61
23 43 0.16
24 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
GGAAGGTTATCAAAATTTCATA
Found at i:2466 original size:23 final size:23
Alignment explanation
Indices: 2418--2497 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
2408 AAATTTGTAG
* *
2418 TTATCAAGATTTCATAAGG-AGG-
1 TTATCAAAATTTTAT-AGGAAGGT
*
2440 TTATTAAAATTTTATAGGGAA-GT
1 TTATCAAAATTTTATA-GGAAGGT
2463 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
2486 TTATCAAAATTT
1 TTATCAAAATTT
2498 CATAACGAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.02
22 19 0.38
23 30 0.60
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:2508 original size:23 final size:22
Alignment explanation
Indices: 2243--2702 Score: 209
Period size: 22 Copynumber: 21.1 Consensus size: 22
2233 CAAAATTCAG
* *
2243 GGAGGATATCAAAATTTCATAT
1 GGAGGTTATCAAAATTTCATAA
*
2265 GAAGGTTATCAAAATTTCAT-A
1 GGAGGTTATCAAAATTTCATAA
* *
2286 GTTTA-GTTTTCAAAATTTCATAA
1 G--GAGGTTATCAAAATTTCATAA
2309 -GAGGGTTATCAAAATTTCAT-A
1 GGA-GGTTATCAAAATTTCATAA
* * * *
2330 GCATGTAGATCAAAATTTCATAG
1 GGAGGT-TATCAAAATTTCATAA
* *
2353 GGAGATTAACAAAATTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* ** *
2375 TGAGGTTATCAAAAAATCATAG
1 GGAGGTTATCAAAATTTCATAA
2397 GGAGGTTATCAAAA-TT--T--
1 GGAGGTTATCAAAATTTCATAA
* *
2414 GTA-GTTATCAAGATTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* * *
2435 GGAGGTTATTAAAATTTTATAG
1 GGAGGTTATCAAAATTTCATAA
* *
2457 GGAAGTTTATCAAAATTTTAT-A
1 GG-AGGTTATCAAAATTTCATAA
2479 GGAAGGTTTATCAAAATTTCATAA
1 GG-AGG-TTATCAAAATTTCATAA
* *
2503 CGAGGTTATCACAATTTCAT-A
1 GGAGGTTATCAAAATTTCATAA
* **
2524 GTATAATTATCAAAATTTCAGT--
1 GGA-GGTTATCAAAATTTCA-TAA
* * *
2546 GTGTGATTA-CTAACAA-TTCATAT
1 G-GAGGTTATC-AA-AATTTCATAA
* * *
2569 GGAGGTTTTTAAATTTTCATAA
1 GGAGGTTATCAAAATTTCATAA
* * ** * * *
2591 CGTGGTTATTGATATATCATAT
1 GGAGGTTATCAAAATTTCATAA
* *
2613 GGAGGTTATCAACATCTCAT-A
1 GGAGGTTATCAAAATTTCATAA
* *
2634 GTGTTGGTTATCAAAATTTCGTAA
1 G-G-AGGTTATCAAAATTTCATAA
* * * * * *
2658 TGAGGTTTTCGAAATTCCTTAG
1 GGAGGTTATCAAAATTTCATAA
*
2680 GGAGGTTAAC-AAATTTCATAA
1 GGAGGTTATCAAAATTTCATAA
2701 GG
1 GG
2703 TTAAAAAAAA
Statistics
Matches: 324, Mismatches: 85, Indels: 59
0.69 0.18 0.13
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 2 0.01
20 1 0.00
21 23 0.07
22 225 0.69
23 57 0.18
24 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GGAGGTTATCAAAATTTCATAA
Found at i:2794 original size:22 final size:22
Alignment explanation
Indices: 2747--2800 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2737 CAATAGTATT
*
2747 GTTATTAAAATTTCATATGAAG
1 GTTATTAAAATTTCATAGGAAG
*
2769 GTTATTAAAATTTTATAAGGAA-
1 GTTATTAAAATTTCAT-AGGAAG
*
2791 GTTATAAAAA
1 GTTATTAAAA
2801 ATAGTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.39
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGAAG
Found at i:3481 original size:16 final size:16
Alignment explanation
Indices: 3460--3497 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3450 TTTCAAAAGC
3460 TTTCATGTATAACTTA
1 TTTCATGTATAACTTA
3476 TTTCATGTATAACTTA
1 TTTCATGTATAACTTA
3492 TTTCAT
1 TTTCAT
3498 TAGCTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.05, T:0.53
Consensus pattern (16 bp):
TTTCATGTATAACTTA
Found at i:3833 original size:33 final size:34
Alignment explanation
Indices: 3796--3862 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
3786 CAAATGTCTG
3796 GTCATTAAGAGAGTTATT-TTTTAGATTTTGCTT
1 GTCATTAAGAGAGTTATTCTTTTAGATTTTGCTT
3829 GTCATTAAGAGAGTTATTCTTTTAGATTTTGCTT
1 GTCATTAAGAGAGTTATTCTTTTAGATTTTGCTT
3863 TCTGCAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 18 0.55
34 15 0.45
ACGTcount: A:0.24, C:0.07, G:0.18, T:0.51
Consensus pattern (34 bp):
GTCATTAAGAGAGTTATTCTTTTAGATTTTGCTT
Found at i:8621 original size:107 final size:105
Alignment explanation
Indices: 8449--8710 Score: 402
Period size: 107 Copynumber: 2.5 Consensus size: 105
8439 AGTTTAGCCT
* **
8449 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAGGGGTAAATTTTAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
8514 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
8556 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
8621 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** * *
8661 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTGAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
8711 TAGAAAAATT
Statistics
Matches: 145, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
103 29 0.20
104 14 0.10
105 36 0.25
107 66 0.46
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:9819 original size:2 final size:2
Alignment explanation
Indices: 9807--9853 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
9797 ATTATTATCC
9807 AT AT A- 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 AT AT
9848 AT AT AT
1 AT AT AT
9854 GTTATAAAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22400 original size:17 final size:17
Alignment explanation
Indices: 22380--22418 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
22370 TTAGTAATAT
22380 TTATTGAATAATAATTA
1 TTATTGAATAATAATTA
** *
22397 TTATTTTATAATTATTA
1 TTATTGAATAATAATTA
22414 TTATT
1 TTATT
22419 TCTGTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTATTGAATAATAATTA
Found at i:22419 original size:17 final size:17
Alignment explanation
Indices: 22387--22419 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22377 TATTTATTGA
22387 ATAATAATTATTATTTT
1 ATAATAATTATTATTTT
*
22404 ATAATTATTATTATTT
1 ATAATAATTATTATTT
22420 CTGTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATAATTATTATTTT
Found at i:25026 original size:60 final size:61
Alignment explanation
Indices: 24919--25038 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 61
24909 CTAGCTAGAG
* *
24919 AATGTGCTAATACATATTGACTTCCTTATTTATAAATTGAAACGTACATAAATCAAATAGGA
1 AATGTGCTAATACA-ATTGACTTCCTTATTTACAAATAGAAACGTACATAAATCAAATAGGA
*
24981 AATGTGCTAATAC-ATTGGCTTCCCTT-TTTACAAATAGAAACGTACATAAATCAAATAG
1 AATGTGCTAATACAATTGACTT-CCTTATTTACAAATAGAAACGTACATAAATCAAATAG
25039 AATTGTCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
60 37 0.69
61 4 0.07
62 13 0.24
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (61 bp):
AATGTGCTAATACAATTGACTTCCTTATTTACAAATAGAAACGTACATAAATCAAATAGGA
Found at i:25249 original size:2 final size:2
Alignment explanation
Indices: 25242--25269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25232 GGTAGAGATA
25242 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
25270 GTAACTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25856 original size:20 final size:20
Alignment explanation
Indices: 25831--25870 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25821 TGCCGTCAGT
25831 ATTTTTTGGGCCACTCAACA
1 ATTTTTTGGGCCACTCAACA
* *
25851 ATTTTTTGGGTCACTTAACA
1 ATTTTTTGGGCCACTCAACA
25871 GATTAGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
ATTTTTTGGGCCACTCAACA
Found at i:25951 original size:2 final size:2
Alignment explanation
Indices: 25944--25968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25934 CAAGGGAAAT
25944 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.