Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019791.1 Corchorus olitorius cultivar O-4 contig19824, 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: 38403
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:847 original size:9 final size:9
Alignment explanation
Indices: 833--858 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
823 TTGAAATAAT
833 TCTTCAAAG
1 TCTTCAAAG
842 TCTTCAAAG
1 TCTTCAAAG
851 TCTTCAAA
1 TCTTCAAA
859 TTATCTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (9 bp):
TCTTCAAAG
Found at i:2034 original size:33 final size:34
Alignment explanation
Indices: 1970--2038 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
1960 TCGAGAGGTC
1970 AGCCCTCAAATTCGTCCTCATCCCAGTACTCGAA
1 AGCCCTCAAATTCGTCCTCATCCCAGTACTCGAA
* *
2004 AGCCCTCAAATTCTTCCTCA-GCCAGTACTCGAA
1 AGCCCTCAAATTCGTCCTCATCCCAGTACTCGAA
2037 AG
1 AG
2039 GTCACTGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.28, C:0.36, G:0.13, T:0.23
Consensus pattern (34 bp):
AGCCCTCAAATTCGTCCTCATCCCAGTACTCGAA
Found at i:2232 original size:11 final size:10
Alignment explanation
Indices: 2211--2267 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
2201 CATTTTTGTA
*
2211 TTTTCTGTTT
1 TTTTCTATTT
2221 TCTTTCTATTT
1 T-TTTCTATTT
2232 TTTTCT-TTT
1 TTTTCTATTT
2241 CTTTTCT-TTT
1 -TTTTCTATTT
*
2251 GTTTTCTATTC
1 -TTTTCTATTT
2262 TTTTCT
1 TTTTCT
2268 TTTATTTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 3 0.07
10 27 0.66
11 11 0.27
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTCTATTT
Found at i:2242 original size:5 final size:5
Alignment explanation
Indices: 2218--2270 Score: 65
Period size: 5 Copynumber: 10.8 Consensus size: 5
2208 GTATTTTCTG
* *
2218 TTTTC -TTTC TATTT- TTTTC TTTTC TTTTC TTTTG TTTTC TATTC TTTTC
1 TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
2267 TTTT
1 TTTT
2271 ATTTGTGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 7 0.17
5 31 0.76
6 3 0.07
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:2246 original size:20 final size:20
Alignment explanation
Indices: 2218--2270 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2208 GTATTTTCTG
2218 TTTTC-TTTCTATTT-TTTTC
1 TTTTCTTTTCT-TTTGTTTTC
2237 TTTTCTTTTCTTTTGTTTTC
1 TTTTCTTTTCTTTTGTTTTC
*
2257 TATTCTTTTCTTTT
1 TTTTCTTTTCTTTT
2271 ATTTGTGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTCTTTTGTTTTC
Found at i:2545 original size:34 final size:34
Alignment explanation
Indices: 2507--2577 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
2497 CTATTAAGTC
*
2507 ATTTGAAAACTAAAACCTGATGGGAACCTTCCCA
1 ATTTGAAAACTAAAACCTGATGAGAACCTTCCCA
*
2541 ATTTGAAAACTAAAACCTGATGAGAACTTTCCCA
1 ATTTGAAAACTAAAACCTGATGAGAACCTTCCCA
2575 ATT
1 ATT
2578 CAAAAAGTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (34 bp):
ATTTGAAAACTAAAACCTGATGAGAACCTTCCCA
Found at i:6337 original size:52 final size:52
Alignment explanation
Indices: 6275--6504 Score: 383
Period size: 52 Copynumber: 4.4 Consensus size: 52
6265 TTTGAAAGCT
*
6275 TAAATTGAATACTTTGAAAACTGATGGTAACTTTCCCAAGTTGAAAATGAGC
1 TAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAAGTTGAAAATGAGC
* *
6327 TAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAATTTGAAAAAGAGC
1 TAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAAGTTGAAAATGAGC
*
6379 TAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAAGTTGAAATTGAGC
1 TAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAAGTTGAAAATGAGC
*
6431 TAAATTGAATACTTTGAAAACTGATGGGAAGC-TTCCCAATTTGAAAAAT-AGC
1 TAAATTGAATACTTTGAAAACTGATGGGAA-CTTTCCCAAGTTG-AAAATGAGC
6483 TAAATTGAATACTTTGAAAACT
1 TAAATTGAATACTTTGAAAACT
6505 TGAATTTCTT
Statistics
Matches: 168, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
52 163 0.97
53 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (52 bp):
TAAATTGAATACTTTGAAAACTGATGGGAACTTTCCCAAGTTGAAAATGAGC
Found at i:6346 original size:25 final size:25
Alignment explanation
Indices: 6315--6398 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
6305 CTTTCCCAAG
6315 TTGAAAATGAGCTAAATTGAATACT
1 TTGAAAATGAGCTAAATTGAATACT
** * **** *
6340 TTGAAAACTGATGGGAACTTTCCCAAT
1 TTGAAAA-TGA-GCTAAATTGAATACT
*
6367 TTGAAAAAGAGCTAAATTGAATACT
1 TTGAAAATGAGCTAAATTGAATACT
6392 TTGAAAA
1 TTGAAAA
6399 CTGATGGGAA
Statistics
Matches: 40, Mismatches: 17, Indels: 4
0.66 0.28 0.07
Matches are distributed among these distances:
25 21 0.52
26 5 0.12
27 14 0.35
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (25 bp):
TTGAAAATGAGCTAAATTGAATACT
Found at i:7561 original size:45 final size:45
Alignment explanation
Indices: 7506--7665 Score: 286
Period size: 45 Copynumber: 3.6 Consensus size: 45
7496 AGTGCATTAC
7506 CTAA-ATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
7550 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
*
7595 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAACAAAG
1 CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
**
7640 CTAATATTCTACTCCTCCATCTCTAG
1 CTAATATTCTACTGATCCATCTCTAG
7666 ATATAAATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
44 4 0.04
45 108 0.96
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (45 bp):
CTAATATTCTACTGATCCATCTCTAGGTAATTCATCAAAATAAAG
Found at i:8040 original size:14 final size:14
Alignment explanation
Indices: 8021--8048 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8011 TTCATCGAGG
8021 ACCTTTTTAGTCAT
1 ACCTTTTTAGTCAT
8035 ACCTTTTTAGTCAT
1 ACCTTTTTAGTCAT
8049 CCGAAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
ACCTTTTTAGTCAT
Found at i:12731 original size:145 final size:145
Alignment explanation
Indices: 12468--12733 Score: 471
Period size: 145 Copynumber: 1.8 Consensus size: 145
12458 AAAAAGTGGC
*
12468 GATATTGTTTGATTGTAGTAAGAGCCATCCATGTGAAGGGATCACCATGGAAAATGTGATGCTGG
1 GATATTGTTTGATTGTAGTAAGAGCCATCCATGTAAAGGGATCACCATGGAAAATGTGATGCTGG
*
12533 ATGGAGAAGGAAATGCAGCAGCCACAGCAACCTGCAACAATGTCCAAGCCACAACTCTAGGGGAT
66 ATGGAGAAGGAAATACAGCAGCCACAGCAACCTGCAACAATGTCCAAGCCACAACTCTAGGGGAT
12598 GTTTCTCCAGGTTGT
131 GTTTCTCCAGGTTGT
* *
12613 GATATTTTTTGATTGTAGTAAGAGCCATCCATGTAAAGGGATCACCATGGAATATGTGATGCTGG
1 GATATTGTTTGATTGTAGTAAGAGCCATCCATGTAAAGGGATCACCATGGAAAATGTGATGCTGG
*
12678 ATGGAGAA-GATAATACAGCAGCCACAGCTACCTGCAACAATGTCCAAGCCACAACT
66 ATGGAGAAGGA-AATACAGCAGCCACAGCAACCTGCAACAATGTCCAAGCCACAACT
12734 GTTAGGATTT
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
144 2 0.02
145 113 0.98
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (145 bp):
GATATTGTTTGATTGTAGTAAGAGCCATCCATGTAAAGGGATCACCATGGAAAATGTGATGCTGG
ATGGAGAAGGAAATACAGCAGCCACAGCAACCTGCAACAATGTCCAAGCCACAACTCTAGGGGAT
GTTTCTCCAGGTTGT
Found at i:14775 original size:32 final size:32
Alignment explanation
Indices: 14738--14815 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
14728 AAGAGTTGTA
14738 TTGTTGTGAGAGAAAGCTAAGATAGCTTTAGG
1 TTGTTGTGAGAGAAAGCTAAGATAGCTTTAGG
14770 TTGTTGTGAGAGAAAGCTAAGATAGCTTTAGG
1 TTGTTGTGAGAGAAAGCTAAGATAGCTTTAGG
14802 TTGTTGTGAGAGAA
1 TTGTTGTGAGAGAA
14816 TCACCCATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.32
Consensus pattern (32 bp):
TTGTTGTGAGAGAAAGCTAAGATAGCTTTAGG
Found at i:15604 original size:26 final size:27
Alignment explanation
Indices: 15575--15625 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
15565 GCATTGGGGT
*
15575 CATCCAGGGGCA-TTTGGTCATTTGTG
1 CATCCAAGGGCATTTTGGTCATTTGTG
*
15601 CATCCAAGGGTATTTTGGTCATTTG
1 CATCCAAGGGCATTTTGGTCATTTG
15626 GTCCCTTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (27 bp):
CATCCAAGGGCATTTTGGTCATTTGTG
Found at i:19359 original size:22 final size:22
Alignment explanation
Indices: 19331--19390 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
19321 TAATTCTTGC
19331 TCTTCAAATAGTTCTTCAAA-AA
1 TCTTCAAATAG-TCTTCAAATAA
*
19353 TCTTC--A-AGTCTTCAAATTA
1 TCTTCAAATAGTCTTCAAATAA
*
19372 TCTTCAAATGGTCTTCAAA
1 TCTTCAAATAGTCTTCAAA
19391 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 8 0.25
19 8 0.25
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTTCAAATAGTCTTCAAATAA
Found at i:19376 original size:19 final size:18
Alignment explanation
Indices: 19343--19378 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19333 TTCAAATAGT
19343 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
19361 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
19379 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:22504 original size:40 final size:40
Alignment explanation
Indices: 22449--23001 Score: 461
Period size: 40 Copynumber: 13.8 Consensus size: 40
22439 TCTGTCTTTC
* * *
22449 CCAGTTTGCCTTTCCTAACTGGAAGGCGTTGTTTTGTTTA
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
*
22489 CCAGTTTTCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
* * **
22529 CCAGTTTGCCTTTCCTAATTGGAAGGTGTTGTTTACATT-
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
** * * *
22568 CTCAGTTTGCCCTTCCCCACTGGAAGGTGTTGTCTAGATTC
1 C-CAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
* * * ** *
22609 CCTGTTTGCCCTTTCTAACTGAAAGGTGTTGTTTACATTC
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
* * *
22649 CCAGTCTACCCTTCCTAACTGGAAGGCGTTGTTTAGTTTA
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
*
22689 CCAGTTTGCCGTTCCTAACTGGAAGGTGTTGTTTAGTTTA
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
** * * ** *
22729 CCAGTTTGCTTTTCCTAACTGGAAGGTATTCTTTACATTC
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
* ** * * *
22769 CCAGTTTGTCCTTCCCCACTGGAAGGTGTTGTCTAGATTC
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
* ** **** ** *
22809 CCTGTTTGCCCTTCCCCACCATTAGGTGTTGTTTAAATTC
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
* * * *
22849 CCAGTTTGCCCTTCCTAATTGGAAGGTGTTCTTT-GCATTC
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAG-TTTA
* **
22889 CCAGTTTGTCCTTCCCCACTGGAAGGTGTTGTTTAGATTCT-
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAG-TT-TA
* ** * * *
22930 CTA-TTTGCTTTTCCTAACTGGAAAGTGTTGTTT-GAATTC
1 CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAG-TTTA
* *
22969 CCAGTCTGCCCTTCCTCA-TCGGAAGGTGTTGTT
1 CCAGTTTGCCCTTCCTAACT-GGAAGGTGTTGTT
23002 CCTATTCCCT
Statistics
Matches: 415, Mismatches: 90, Indels: 16
0.80 0.17 0.03
Matches are distributed among these distances:
38 1 0.00
39 7 0.02
40 401 0.97
41 5 0.01
42 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (40 bp):
CCAGTTTGCCCTTCCTAACTGGAAGGTGTTGTTTAGTTTA
Found at i:22582 original size:80 final size:80
Alignment explanation
Indices: 22446--23001 Score: 564
Period size: 80 Copynumber: 7.0 Consensus size: 80
22436 TTATCTGTCT
* *** * * *
22446 TTCCCAGTTTGCCTTTCCTAACTGGAAGGCGTTGTTTTGTTTACCAGTTTTCCCTTCCTAACTGG
1 TTCCCAGTTTGCCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTGG
*
22511 AAGGTGTTGTTTAGT
66 AAGGTGTTGTTTAGA
* * * *
22526 TTACCAGTTTGCCTTTCCTAATTGGAAGGTGTTGTTTACATTCTCAGTTTGCCCTTCCCCACTGG
1 TTCCCAGTTTGCCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTGG
*
22591 AAGGTGTTGTCTAGA
66 AAGGTGTTGTTTAGA
* * * * *
22606 TTCCCTGTTTGCCCTTT-CTAACTGAAAGGTGTTGTTTACATTCCCAGTCTACCCTTCCTAACTG
1 TTCCCAGTTTG-CCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTG
* *
22670 GAAGGCGTTGTTTAGT
65 GAAGGTGTTGTTTAGA
* * ** * ** *
22686 TTACCAGTTTGCCGTTCCTAACTGGAAGGTGTTGTTTAGTTTACCAGTTTGCTTTTCCTAACTGG
1 TTCCCAGTTTGCCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTGG
* * *
22751 AAGGTATTCTTTACA
66 AAGGTGTTGTTTAGA
** * * * * **
22766 TTCCCAGTTTGTCC-TTCCCCACTGGAAGGTGTTGTCTAGATTCCCTGTTTGCCCTTCCCCACCA
1 TTCCCAGTTTG-CCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTG
** *
22830 TTAGGTGTTGTTTAAA
65 GAAGGTGTTGTTTAGA
* * * * * *
22846 TTCCCAGTTTGCCCTTCCTAATTGGAAGGTGTTCTTTGCATTCCCAGTTTGTCCTTCCCCACTGG
1 TTCCCAGTTTGCCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTGG
22911 AAGGTGTTGTTTAGA
66 AAGGTGTTGTTTAGA
* * * *
22926 TTCTCTA-TTTGCTTTTCCTAACTGGAAAGTGTTGTTTGA-ATTCCCAGTCTGCCCTTCCTCA-T
1 TTC-CCAGTTTGCCTTTCCTAACTGGAAGGTGTTGTTT-ACATTCCCAGTTTGCCCTTCCTCACT
22988 CGGAAGGTGTTGTT
64 -GGAAGGTGTTGTT
23002 CCTATTCCCT
Statistics
Matches: 386, Mismatches: 83, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
79 7 0.02
80 370 0.96
81 9 0.02
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (80 bp):
TTCCCAGTTTGCCTTTCCTAACTGGAAGGTGTTGTTTACATTCCCAGTTTGCCCTTCCTCACTGG
AAGGTGTTGTTTAGA
Found at i:22664 original size:120 final size:120
Alignment explanation
Indices: 22450--22998 Score: 539
Period size: 120 Copynumber: 4.6 Consensus size: 120
22440 CTGTCTTTCC
* * * * * *
22450 CAGTTTGCCTTTCCTAACTGGAAGGCGTTGTTTTGTTTACCAGTTTTCCCTTCCTAACTGGAAGG
1 CAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTACCAGTTTGCCCTTCCTAACTGGAAGG
* ** * * * * *
22515 TGTTGTTTAGTTTACCAGTTTGCCTTTCCTAATTGGAAGGTGTTGTTTACATTCT
66 TGTTCTTTACATTCCCAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTCT
* * * * * *
22570 CAGTTTGCCCTTCCCCACTGGAAGGTGTTGTCTAGATTCCCTGTTTGCCCTTTCTAACTGAAAGG
1 CAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTACCAGTTTGCCCTTCCTAACTGGAAGG
* * * * * *
22635 TGTTGTTTACATTCCCAGTCTACCCTTCCTAACTGGAAGGCGTTGTTTAGTTTAC-
66 TGTTCTTTACATTCCCAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATT-CT
* * * **
22690 CAGTTTGCCGTTCCTAACTGGAAGGTGTTGTTTAGTTTACCAGTTTGCTTTTCCTAACTGGAAGG
1 CAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTACCAGTTTGCCCTTCCTAACTGGAAGG
* * * * *
22755 TATTCTTTACATTCCCAGTTTGTCCTTCCCCACTGGAAGGTGTTGTCTAGATTCC
66 TGTTCTTTACATTCCCAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTCT
* * **** * * *
22810 CTGTTTGCCCTTCCCCACCATTAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTAATTGGAAGG
1 CAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTACCAGTTTGCCCTTCCTAACTGGAAGG
* * *
22875 TGTTCTTTGCATTCCCAGTTTGTCCTTCCCCACTGGAAGGTGTTGTTTAGATTCT
66 TGTTCTTTACATTCCCAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTCT
** * * * * *
22930 CTA-TTTGCTTTTCCTAACTGGAAAGTGTTGTTT-GAATTCCCAGTCTGCCCTTCCTCA-TCGGA
1 C-AGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAG-ATTACCAGTTTGCCCTTCCTAACT-GGA
22992 AGGTGTT
63 AGGTGTT
22999 GTTCCTATTC
Statistics
Matches: 350, Mismatches: 74, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
119 2 0.01
120 347 0.99
121 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (120 bp):
CAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTACCAGTTTGCCCTTCCTAACTGGAAGG
TGTTCTTTACATTCCCAGTTTGCCCTTCCCAACTGGAAGGTGTTGTTTAGATTCT
Found at i:27089 original size:36 final size:35
Alignment explanation
Indices: 26981--27179 Score: 258
Period size: 35 Copynumber: 5.6 Consensus size: 35
26971 ATTCAAGTTC
*
26981 TTTTCAAATTGGGAAAGTTCCCATCAG-TTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
*
27015 TTTTCAAATGGGGAAAGTTCCCACCAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
*
27050 TTTTTAAATTGGGAAAGTTCCCACCAGTTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCACCAG-TTTTTAAG
*
27086 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCA-CCAGTTTT-TAAG
* ** * *
27123 TTTTCAAATTGGAAAAGTTCCCATAAGGTTTTCA-
1 TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
*
27157 TTTTCAATTTAGGGAAAGTTCCC
1 TTTTCAAATT-GGGAAAGTTCCC
27180 GTCATTTTCA
Statistics
Matches: 146, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
34 34 0.23
35 44 0.30
36 39 0.27
37 29 0.20
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
Found at i:31232 original size:25 final size:26
Alignment explanation
Indices: 31197--31245 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
31187 TTGGGAAATC
*
31197 TTTCAATTGATGTTAGGATTATATAT
1 TTTCAATTGATGTTAGGATAATATAT
31223 TTTC-ATTGATGTTAGGATAATAT
1 TTTCAATTGATGTTAGGATAATAT
31246 TCAACATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (26 bp):
TTTCAATTGATGTTAGGATAATATAT
Found at i:32692 original size:22 final size:22
Alignment explanation
Indices: 32660--32760 Score: 100
Period size: 22 Copynumber: 4.5 Consensus size: 22
32650 GCTCCAGCGA
*
32660 AAAATATTGATAACCACATTGTG
1 AAAAT-TTGATAACCACATTATG
*
32683 AAAATTTGATAACCTCATTATG
1 AAAATTTGATAACCACATTATG
*
32705 -AAATTTCGATAACCTC-TCTATG
1 AAAATTT-GATAACCACAT-TATG
* *
32727 AAAATTTGATAACCACACTGT-
1 AAAATTTGATAACCACATTATG
32748 AAAATTTTGATAA
1 AAAA-TTTGATAA
32761 TAATAATCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
21 11 0.16
22 46 0.68
23 11 0.16
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.34
Consensus pattern (22 bp):
AAAATTTGATAACCACATTATG
Found at i:32856 original size:22 final size:20
Alignment explanation
Indices: 32828--32990 Score: 141
Period size: 22 Copynumber: 7.6 Consensus size: 20
32818 ACCTAATTCC
32828 TGAAATTTTGATAATCACTCTA
1 TGAAATTTTGATAA-C-CTCTA
32850 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACC-TC-TA
* *
32872 TGAAATTTTGGTAACCACAATA
1 TGAAATTTTGATAACCTC--TA
* *
32894 TGAATTTTTTATAACCTCCCTA
1 TGAAATTTTGATAACCT--CTA
* *
32916 TAAAATTTTG-TAACCGAACTA
1 TGAAATTTTGATAACC--TCTA
32937 TGAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAACCT-C-TA
32959 TGAAATTTTTGATAACCTC-A
1 TGAAA-TTTTGATAACCTCTA
32979 TGAAATTTTGAT
1 TGAAATTTTGAT
32991 TACCAAACAA
Statistics
Matches: 118, Mismatches: 12, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.06
20 7 0.06
21 22 0.19
22 69 0.58
23 12 0.10
24 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
TGAAATTTTGATAACCTCTA
Found at i:32896 original size:44 final size:44
Alignment explanation
Indices: 32828--32967 Score: 167
Period size: 44 Copynumber: 3.2 Consensus size: 44
32818 ACCTAATTCC
* * * *
32828 TGAAATTTTGATAATCACTCTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCATA
* * * *
32872 TGAAATTTTGGTAACCACAATATGAATTTTTTATAACCTCCCTA
1 TGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCATA
* *
32916 TAAAATTTT-GTAACCGA-ACTATGAAATTTTGATAACCTCCTTA
1 TGAAATTTTGGTAACC-ACACTATGAAATTTTGATAACCTCCATA
32959 TGAAATTTT
1 TGAAATTTT
32968 TGATAACCTC
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
43 36 0.44
44 45 0.56
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (44 bp):
TGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCCATA
Found at i:33736 original size:22 final size:22
Alignment explanation
Indices: 33711--34302 Score: 330
Period size: 22 Copynumber: 26.5 Consensus size: 22
33701 TAGTGTGATC
* *
33711 ATCAAAATTTCATACTGAGGTA
1 ATCAAAATTTCATAGTGAGGTT
* *
33733 ATCAAAATTTCACAGTGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
* *
33755 ATCAAACTTTCATATGGATTAGGTT
1 ATCAAAATTTCATA--G-TGAGGTT
* *
33780 ATTC-AAATTTCATACG-AAAGTT
1 A-TCAAAATTTCATA-GTGAGGTT
*
33802 ATCAAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
*
33824 ATCAAAATTTCATAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* **
33846 ATCAAAATTCCATAGCAAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
33868 ATCAGAATTTCATAGTGTGGGT
1 ATCAAAATTTCATAGTGAGGTT
*
33890 ATCAAAATTTTATAAG-GAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
*
33912 ATCAAAGATTTCATAGTGTGGTT
1 ATCAAA-ATTTCATAGTGAGGTT
* ** *
33935 ACCAAAATCTAAATTTAATACGAAGGTT
1 ATCAAAAT-TTCA--TAGT--G-AGGTT
33963 ATCAAAATGTT-ATAGTGTA-GTT
1 ATCAAAAT-TTCATAGTG-AGGTT
* * **
33985 ATCAAAATTTCATCA-AGAAGCA
1 ATCAAAATTTCAT-AGTGAGGTT
* * *
34007 ATCAAAATCTCATAGAGTA-CTT
1 ATCAAAATTTCATAGTG-AGGTT
* * * * *
34029 TTCAAAAATCCATAGATCAGATT
1 ATCAAAATTTCATAG-TGAGGTT
* **
34052 ACCAAAATTTCATAG-GATAATT
1 ATCAAAATTTCATAGTGA-GGTT
* *
34074 ATCAAAA-TTCATAATGTGGTT
1 ATCAAAATTTCATAGTGAGGTT
**
34095 ATCAAAATTTCATAGAAAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
34117 ATCAAAATTTTAAAGCGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
** *
34139 ATCAAAATTTCCCAGTGAAGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
34161 ATGAAAAATTTTCATATTGTGGTT
1 AT-CAAAA-TTTCATAGTGAGGTT
*
34185 ATTAAAATTTCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
*
34207 -TC-AAATTTCATAGT-ATGATT
1 ATCAAAATTTCATAGTGA-GGTT
*
34227 ATCAAAATTTCATAGAGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * *
34249 AGCAACATTTCATTG-GAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* ***
34271 ATCAAAATTTCATAATGTTATT
1 ATCAAAATTTCATAGTGAGGTT
34293 ATCAAAATTT
1 ATCAAAATTT
34303 TAGAGTGTGG
Statistics
Matches: 433, Mismatches: 102, Indels: 70
0.72 0.17 0.12
Matches are distributed among these distances:
19 1 0.00
20 13 0.03
21 29 0.07
22 292 0.67
23 47 0.11
24 14 0.03
25 21 0.05
26 2 0.00
27 2 0.00
28 12 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:34108 original size:43 final size:42
Alignment explanation
Indices: 34054--34241 Score: 130
Period size: 42 Copynumber: 4.3 Consensus size: 42
34044 ATCAGATTAC
34054 CAAAATTTCATAGGATAATTATCAAAATTCATAATGTGGTTAT
1 CAAAATTTCATAGGA-AATTATCAAAATTCATAATGTGGTTAT
* * *
34097 CAAAATTTCATA-GAAAGGTTATCAAAATT-TTAAAGCGAGGTTAT
1 CAAAATTTCATAGGAAA--TTATCAAAATTCAT-AA-TGTGGTTAT
** * * *
34141 CAAAATTTCCCAGTGAAGTTATGAAAAATTTTCATATTGTGGTTAT
1 CAAAATTTCATAG-GAAATTAT-CAAAA--TTCATAATGTGGTTAT
* ** * * * *
34187 TAAAATTTCATATGGAGGTT-TCAAATTTCATAGTATGATTAT
1 CAAAATTTCATA-GGAAATTATCAAAATTCATAATGTGGTTAT
34229 CAAAATTTCATAG
1 CAAAATTTCATAG
34242 AGAGGTTAGC
Statistics
Matches: 113, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
41 3 0.03
42 27 0.24
43 25 0.22
44 24 0.21
45 5 0.04
46 24 0.21
47 4 0.04
48 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (42 bp):
CAAAATTTCATAGGAAATTATCAAAATTCATAATGTGGTTAT
Found at i:34510 original size:44 final size:44
Alignment explanation
Indices: 34478--34572 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
34468 GGATGTTAAT
*
34478 AAAATTTCATATTGAAGTTATCGAAAAATCATAGGAAGGTTATC
1 AAAATTTCATAATGAAGTTATCGAAAAATCATAGGAAGGTTATC
* *
34522 AAAATTTCATAATGAAGTTATCGAAAAATCATAGAAAGATTATC
1 AAAATTTCATAATGAAGTTATCGAAAAATCATAGGAAGGTTATC
34566 AAAATTT
1 AAAATTT
34573 GTGATTATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (44 bp):
AAAATTTCATAATGAAGTTATCGAAAAATCATAGGAAGGTTATC
Found at i:34605 original size:22 final size:22
Alignment explanation
Indices: 34450--34660 Score: 95
Period size: 22 Copynumber: 9.8 Consensus size: 22
34440 CAAAATTGGG
* * * *
34450 GTTATAAAAACTTCATAGGGAT
1 GTTATCAAAATTTCATAAGGAA
**
34472 GTTAAT-AAAATTTCATATTGAA
1 GTT-ATCAAAATTTCATAAGGAA
*
34494 GTTATCGAAAA-ATCAT-AGGAA
1 GTTATC-AAAATTTCATAAGGAA
*
34515 GGTTATCAAAATTTCATAATGAA
1 -GTTATCAAAATTTCATAAGGAA
* *
34538 GTTATCGAAAA-ATCAT-AGAAA
1 GTTATC-AAAATTTCATAAGGAA
*
34559 GATTATCAAAATTT-GT---G-A
1 G-TTATCAAAATTTCATAAGGAA
*
34577 -TTATCAAAATTTCATAAGGAT
1 GTTATCAAAATTTCATAAGGAA
** * *
34598 GTTATCAAAATTTTTTAGGGAG
1 GTTATCAAAATTTCATAAGGAA
* *
34620 GTTTATCAAAATTTTAT-ATGAA
1 G-TTATCAAAATTTCATAAGGAA
*
34642 TGTTTATCGAAATTTCATA
1 -G-TTATCAAAATTTCATA
34661 CCGAGGTCAT
Statistics
Matches: 144, Mismatches: 27, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
16 12 0.08
17 1 0.01
18 1 0.01
20 1 0.01
21 18 0.12
22 68 0.47
23 43 0.30
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAA
Found at i:34646 original size:23 final size:23
Alignment explanation
Indices: 34577--34656 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
34567 AAATTTGTGA
*
34577 TTATCAAAATTTCATAAGGATG-
1 TTATCAAAATTTTATAAGGATGT
* * *
34599 TTATCAAAATTTTTTAGGGAGGT
1 TTATCAAAATTTTATAAGGATGT
* *
34622 TTATCAAAATTTTATATGAATGT
1 TTATCAAAATTTTATAAGGATGT
*
34645 TTATCGAAATTT
1 TTATCAAAATTT
34657 CATACCGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 18 0.38
23 30 0.62
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGGATGT
Found at i:34711 original size:22 final size:22
Alignment explanation
Indices: 34572--34811 Score: 76
Period size: 22 Copynumber: 10.8 Consensus size: 22
34562 TATCAAAATT
34572 TGTGATTATCAAAATTTCATAAG
1 TGTGATTATCAAAATTTCAT-AG
**
34595 -GATG-TTATCAAAATTTTTTAG
1 TG-TGATTATCAAAATTTCATAG
* * * *
34616 GGAGGTTTATCAAAATTTTATA-
1 TG-TGATTATCAAAATTTCATAG
* * *
34638 TGAATGTTTATCGAAATTTCATAC
1 TG--TGATTATCAAAATTTCATAG
* * * * * * *
34662 CGAGGTCATTACAATTTTATAG
1 TGTGATTATCAAAATTTCATAG
* *
34684 TTTGATTATCAAAATTTCACAG
1 TGTGATTATCAAAATTTCATAG
* *
34706 TGTGATCA-CTAAGATTTCATAG
1 TGTGATTATC-AAAATTTCATAG
* * * * **
34728 GGAGGTTATAAAAAATAGCATAG
1 TGTGATTAT-CAAAATTTCATAG
* * *
34751 TGTGATTACCAACATTTCA-CG
1 TGTGATTATCAAAATTTCATAG
* *
34772 TGAAGATTATCAAAATTTTATAG
1 TG-TGATTATCAAAATTTCATAG
* *
34795 TGCGCTTATCAAAATTT
1 TGTGATTATCAAAATTT
34812 AAGTGGATAT
Statistics
Matches: 153, Mismatches: 54, Indels: 21
0.67 0.24 0.09
Matches are distributed among these distances:
21 6 0.04
22 95 0.62
23 51 0.33
24 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
TGTGATTATCAAAATTTCATAG
Found at i:35826 original size:1 final size:1
Alignment explanation
Indices: 35820--35849 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
35810 GCCTAATTAC
35820 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35850 CCAACAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37339 original size:11 final size:11
Alignment explanation
Indices: 37304--37360 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
37294 TCATGCACCC
37304 AAAACATTTAT
1 AAAACATTTAT
37315 CAAAACATTTTAT
1 -AAAACA-TTTAT
*
37328 AAAGCATTTAT
1 AAAACATTTAT
* *
37339 ATAAATCAGTAAT
1 A-AAA-CATTTAT
37352 AAAACATTT
1 AAAACATTT
37361 CCTCAACGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
11 9 0.25
12 16 0.44
13 11 0.31
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35
Consensus pattern (11 bp):
AAAACATTTAT
Done.