Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011041.1 Kokia drynarioides strain JFW-HI SEQ_126012, 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: 389353
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:371125 original size:23 final size:23
Alignment explanation
Indices: 371063--371125 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
371053 ATTTAGTTAT
* *
371063 TTAATAAAATTTATGTATAATTAA
1 TTAAT-AAATTCATGTGTAATTAA
*
371087 TTGATAAATTCATGTGTAATTAA
1 TTAATAAATTCATGTGTAATTAA
371110 TTAATAAATTCATGTG
1 TTAATAAATTCATGTG
371126 AAAGGAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
23 31 0.89
24 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (23 bp):
TTAATAAATTCATGTGTAATTAA
Found at i:373294 original size:29 final size:28
Alignment explanation
Indices: 373261--373602 Score: 382
Period size: 30 Copynumber: 11.7 Consensus size: 28
373251 AATTCGAGGT
* *
373261 TAAAAATGGAATTCTTAGACA-TTCGGGG
1 TAAAAATGGAATTTTTGGA-AGTTCGGGG
* *
373289 TAAAAATGGAATTTTTGGAAGTTTTGTGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
*
373318 TCAAAAATGGAATTTTTGGAAGTTTCGTGG
1 T-AAAAATGGAATTTTTGGAAG-TTCGGGG
* *
373348 TCAAAAATAGAATTTTTGGAAGTTTGGGCG
1 T-AAAAATGGAATTTTTGGAAGTTCGGG-G
* * *
373378 TAAAAATAGAATTTTTAGAAGTTTCGAGGT
1 TAAAAATGGAATTTTTGGAAG-TTCG-GGG
*
373408 TAAAAATAGAATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTC-GGGG
373437 TAAAAATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
*
373466 TCAAAAATGGAATTCTTGGAAGTTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTCG-GGG
* **
373496 TAAAAATGGAATTTTTCGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
373525 TAAAAATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAG-TTCGGGG
*
373554 TCAAAAATGGAATTTTTTGAAGTTCGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTC-GGGG
373584 TAAAAATGGAA-TTTTGGAA
1 TAAAAATGGAATTTTTGGAA
373603 TTTTCGAGGT
Statistics
Matches: 277, Mismatches: 24, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
27 1 0.00
28 24 0.09
29 124 0.45
30 126 0.45
31 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAAGTTCGGGG
Found at i:373305 original size:59 final size:57
Alignment explanation
Indices: 373253--373611 Score: 377
Period size: 59 Copynumber: 6.1 Consensus size: 57
373243 TTTGGGAAAA
* *
373253 TTCGAGGTTAAAAATGGAATTCTTAGACA-TTCGGGGTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGA-AGTTCGGGGTAAAAATGGAATTTTTGGAAG
* * * * *
373310 TTTTG-TGGTCAAAAATGGAATTTTTGGAAGTTTCGTGGTCAAAAATAGAATTTTTGGAAG
1 -TTCGAGGGT-AAAAATGGAATTTTTAGAAG-TTCGGGGT-AAAAATGGAATTTTTGGAAG
* * * *
373370 TTTG-GGCGTAAAAATAGAATTTTTAGAAGTTTCGAGGTTAAAAATAGAATTTTTGGAAG
1 TTCGAGG-GTAAAAATGGAATTTTTAGAAG-TTCG-GGGTAAAAATGGAATTTTTGGAAG
* * *
373429 TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTCTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAG-TTCGGGGT-AAAAATGGAATTTTTGGAAG
* **
373488 TTCGAGGGTAAAAATGGAATTTTTCGAAGTTTTAGGGTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAG-TTCGGGGTAAAAATGGAATTTTTGGAAG
* *
373546 TTTCG-GGGTCAAAAATGGAATTTTTTGAAGTTCGGGGGTAAAAATGGAA-TTTTGGAATT
1 -TTCGAGGGT-AAAAATGGAATTTTTAGAAGTTC-GGGGTAAAAATGGAATTTTTGGAA-G
373605 TTCGAGG
1 TTCGAGG
373612 TCTACTGGGC
Statistics
Matches: 261, Mismatches: 27, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
57 3 0.01
58 59 0.23
59 174 0.67
60 25 0.10
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (57 bp):
TTCGAGGGTAAAAATGGAATTTTTAGAAGTTCGGGGTAAAAATGGAATTTTTGGAAG
Found at i:373326 original size:30 final size:29
Alignment explanation
Indices: 373261--373608 Score: 413
Period size: 29 Copynumber: 11.9 Consensus size: 29
373251 AATTCGAGGT
* *
373261 TAAAAATGGAATTCTTAGACA--TTCGGGG
1 TAAAAATGGAATTTTTGGA-AGTTTCGGGG
* *
373289 TAAAAATGGAATTTTTGGAAGTTTTGTGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
373318 TCAAAAATGGAATTTTTGGAAGTTTCGTGG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGGG
*
373348 TCAAAAATAGAATTTTTGGAAGTTT-GGGCG
1 T-AAAAATGGAATTTTTGGAAGTTTCGGG-G
* * *
373378 TAAAAATAGAATTTTTAGAAGTTTCGAGGT
1 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
*
373408 TAAAAATAGAATTTTTGGAAG-TTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTTTC-GGGG
373437 TAAAAATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
373466 TCAAAAATGGAATTCTTGGAAG-TTCGAGGG
1 T-AAAAATGGAATTTTTGGAAGTTTCG-GGG
* **
373496 TAAAAATGGAATTTTTCGAAGTTTTAGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
373525 TAAAAATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGAATTTTTGGAAGTTTCGGGG
*
373554 TCAAAAATGGAATTTTTTGAAG-TTCGGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTC-GGGG
*
373584 TAAAAATGGAA-TTTTGGAATTTTCG
1 TAAAAATGGAATTTTTGGAAGTTTCG
373609 AGGTCTACTG
Statistics
Matches: 283, Mismatches: 23, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
27 1 0.00
28 25 0.09
29 128 0.45
30 127 0.45
31 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAGTTTCGGGG
Found at i:373354 original size:88 final size:87
Alignment explanation
Indices: 373253--373612 Score: 403
Period size: 88 Copynumber: 4.1 Consensus size: 87
373243 TTTGGGAAAA
* * * *
373253 TTCGAGGTTAAAAATGGAATTCTTAGACA-TTCGGGGT-AAAAATGGAATTTTTGGAAGTTTTGT
1 TTCGAGG-TAAAAATGGAATTTTTGGA-AGTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCGG
373316 GGTCAAAAATGGAATTTTTGGAAGT
64 GGT-AAAAATGGAATTTTTGGAAGT
* * * * *
373341 TTCGTGGTCAAAAATAGAATTTTTGGAAGTTTGGGCGT-AAAAATAGAATTTTTAGAAGTTTCGA
1 TTCGAGGT-AAAAATGGAATTTTTGGAAGTTCGGG-GTCAAAAATGGAATTTTTGGAAGTTTCG-
* *
373405 GGTTAAAAATAGAATTTTTGGAAG-
63 GGGTAAAAATGGAATTTTTGGAAGT
* *
373429 TTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTCTTGGAAG-TTCGA
1 TTC-GAGGTAAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCG-
*
373493 GGGTAAAAATGGAATTTTTCGAAGT
63 GGGTAAAAATGGAATTTTTGGAAGT
* *
373518 TT-TAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTTGAAG-TTCGG
1 TTCGA-GGTAAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTC-G
*
373581 GGGTAAAAATGGAA-TTTTGGAATT
63 GGGTAAAAATGGAATTTTTGGAAGT
373605 TTCGAGGT
1 TTCGAGGT
373613 CTACTGGGCA
Statistics
Matches: 234, Mismatches: 27, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
87 15 0.06
88 145 0.62
89 72 0.31
90 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (87 bp):
TTCGAGGTAAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGG
TAAAAATGGAATTTTTGGAAGT
Found at i:375401 original size:17 final size:17
Alignment explanation
Indices: 375381--375484 Score: 112
Period size: 17 Copynumber: 6.4 Consensus size: 17
375371 CTTTATTTAT
* *
375381 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
375398 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
375416 TTTAAA-CT----TAAA
1 TTTAAATTTAAAATAAA
375428 -TTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
375444 TTTAAATTTTAAAATAAA
1 TTTAAA-TTTAAAATAAA
*
375462 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
375479 TTTAAA
1 TTTAAA
375485 ATGAGTTTGG
Statistics
Matches: 73, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
11 5 0.07
12 5 0.07
16 4 0.05
17 31 0.42
18 28 0.38
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:375435 original size:46 final size:46
Alignment explanation
Indices: 375382--375486 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
375372 TTTATTTATT
* *
375382 TTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAA
1 TTAAATTTAAAATAAATTTAAATTTGAAAATAAATTTAAACTTAAA
* **
375428 TTAAATTTAAAATAAATTTAAATTTTAAAATAAATTTAATTTTAAA
1 TTAAATTTAAAATAAATTTAAATTTGAAAATAAATTTAAACTTAAA
*
375474 ATAAATTTAAAAT
1 TTAAATTTAAAAT
375487 GAGTTTGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (46 bp):
TTAAATTTAAAATAAATTTAAATTTGAAAATAAATTTAAACTTAAA
Found at i:375437 original size:11 final size:12
Alignment explanation
Indices: 375381--375484 Score: 69
Period size: 11 Copynumber: 9.0 Consensus size: 12
375371 CTTTATTTAT
375381 TTTAAATTTATAA
1 TTTAAATTTA-AA
*
375394 --TAATTTTAAA
1 TTTAAATTTAAA
*
375404 TTTGAAA-ATAAA
1 TTT-AAATTTAAA
*
375416 TTTAAACTTAAA
1 TTTAAATTTAAA
375428 -TTAAATTTAAA
1 TTTAAATTTAAA
*
375439 -ATAAATTTAAA
1 TTTAAATTTAAA
*
375450 TTTTAAA-ATAAA
1 -TTTAAATTTAAA
*
375462 TTTAATTTTAAA
1 TTTAAATTTAAA
*
375474 -ATAAATTTAAA
1 TTTAAATTTAAA
375485 ATGAGTTTGG
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
10 2 0.03
11 44 0.61
12 20 0.28
13 6 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:375437 original size:35 final size:33
Alignment explanation
Indices: 375381--375484 Score: 110
Period size: 35 Copynumber: 3.2 Consensus size: 33
375371 CTTTATTTAT
*
375381 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTA-AATAAATTTAAATTT-AAAATAAA
*
375416 TTTAAA-CT---TAAA-TTAAATTTAAAATAAA
1 TTTAAATTTAAATAAATTTAAATTTAAAATAAA
*
375444 TTTAAATTTTAAAATAAATTTAATTTTAAAATAAA
1 TTTAAA-TTT-AAATAAATTTAAATTTAAAATAAA
375479 TTTAAA
1 TTTAAA
375485 ATGAGTTTGG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
28 14 0.24
29 8 0.14
30 4 0.07
34 5 0.09
35 27 0.47
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
TTTAAATTTAAATAAATTTAAATTTAAAATAAA
Found at i:375454 original size:7 final size:6
Alignment explanation
Indices: 375381--375484 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
375371 CTTTATTTAT
* * *
375381 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * *
375428 -TTAAA TTTAAA -ATAAA TTTAAA TTTTAAA -ATAAA TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
*
375474 -ATAAA TTTAAA
1 TTTAAA TTTAAA
375485 ATGAGTTTGG
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
4 1 0.01
5 22 0.29
6 41 0.55
7 11 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:375455 original size:29 final size:28
Alignment explanation
Indices: 375399--375466 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 28
375389 TATAATAATT
375399 TTAAATTTGAAAATAAATTTAAACTTAAA
1 TTAAATTT-AAAATAAATTTAAACTTAAA
*
375428 TTAAATTTAAAATAAATTTAAATTTTAAA
1 TTAAATTTAAAATAAATTTAAA-CTTAAA
*
375457 ATAAATTTAA
1 TTAAATTTAA
375467 TTTTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TTAAATTTAAAATAAATTTAAACTTAAA
Found at i:376232 original size:205 final size:207
Alignment explanation
Indices: 375813--376261 Score: 535
Period size: 205 Copynumber: 2.2 Consensus size: 207
375803 TCTGGTTTCA
* * * * ***
375813 TTGACTTGGCCTTCTTCTCAGTATCTCATCAAGAAGGTGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTACAATCCACTT
*** ** * * **
375878 CTCTGTGTTTCATCAGGAAGACGGATTTGATTCACTTTTTTGTATCTCAATCAAGGAGCTAACTA
66 CTCTGTACCTCATCAGGAAGACAAATTTGATCCACTTCTCAGTATCTCAATCAAGGAGCTAAC-A
* * * * * * *
375943 TTTTTATTACTTTGGCTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCAT
130 CTTTTATTACTTCGACATGCTTCTCAGTATCTCACCAGGAAGCTGGGGTTCAAAGATTTACTCAC
376008 ATCGAGCGCGGGT
195 ATCGAGCGCGGGT
* * ** *
376021 TTGATTTGGTCTTCTTCTCATTATCTCATCAGGAAGATGACCGCGTCGTTTGTTACAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTACAATCCACTT
*
376086 CTCTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTC-ATC-AGGAAGCTAAC-
66 CTCTGTACCTCATCAGGAAGACAAATTTGATCCACTTCTCAGTATCTCAATCAAGG-AGCTAACA
* * * * *
376148 CTTTTATTGCTTCGACATGCTTCTCGGTGTCTTACCAGGAAGCTGGGGTTCGAAGATTTACTCAC
130 CTTTTATTACTTCGACATGCTTCTCAGTATCTCACCAGGAAGCTGGGGTTCAAAGATTTACTCAC
*
376213 ATCGAGCGTGGGT
195 ATCGAGCGCGGGT
*
376226 TTGATTTGGTTTTCTTCTCAGTATCTCATCAGGAAG
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
376262 CTAACATTTT
Statistics
Matches: 203, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
205 99 0.49
206 3 0.01
207 10 0.05
208 91 0.45
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (207 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTACAATCCACTT
CTCTGTACCTCATCAGGAAGACAAATTTGATCCACTTCTCAGTATCTCAATCAAGGAGCTAACAC
TTTTATTACTTCGACATGCTTCTCAGTATCTCACCAGGAAGCTGGGGTTCAAAGATTTACTCACA
TCGAGCGCGGGT
Found at i:376321 original size:119 final size:119
Alignment explanation
Indices: 376120--376380 Score: 495
Period size: 119 Copynumber: 2.2 Consensus size: 119
376110 ATTTGGTCCA
* * *
376120 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACATGCTTCTCGGTGTCTTACCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTACTTCAACATGCTTCTCGGTGTCTTACCA
376185 GGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTT
66 GGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTT
376239 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTACTTCAACATGCTTCTCGGTGTCTTACCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTACTTCAACATGCTTCTCGGTGTCTTACCA
376304 GGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTT
66 GGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTT
376358 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
376381 ATATCCGCAT
Statistics
Matches: 139, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
119 139 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (119 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTACTTCAACATGCTTCTCGGTGTCTTACCA
GGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTT
Found at i:376465 original size:204 final size:204
Alignment explanation
Indices: 376239--376806 Score: 895
Period size: 204 Copynumber: 2.8 Consensus size: 204
376229 ATTTGGTTTT
* * * * * *
376239 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTACTTCAACATGCTTCTCGGTGTCTTACCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCA
* * * * *
376304 GGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTTCTTCTCAGTAT
66 GGAAGCTAGGGTTCGAAGATTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTAT
*
376369 CTCATCAGGAAGAT-ATCCGCATCGCTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGATGA
131 CTCATCAGGAAGATGA-CCGCATCGCTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGACGA
376433 ATTTGGTCCA
195 ATTTGGTCCA
*
376443 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCA
* * *
376508 AGAAGCTAGGGTTCAAAGATTTGCTCATACCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTAGGGTTCGAAGATTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTAT
* * *
376573 CTCATCAGGAAAATGACTGCATCGCTGTTTTAATTCGCTTCTCTGTATCTCATTAGGAAGACGAA
131 CTCATCAGGAAGATGACCGCATCGCTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGACGAA
376638 TTTGGTCCA
196 TTTGGTCCA
*
376647 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCACCCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCA
* * * * *
376712 GGAAACTAAGGTTCGAAGATTTGTTCATATCGAGCACGGGTTTGGTTTGGTCTTCTTCTCAGTAT
66 GGAAGCTAGGGTTCGAAGATTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTAT
376777 CTCATCAGGAAGATGACCGCATCGCTGTTT
131 CTCATCAGGAAGATGACCGCATCGCTGTTT
376807 GTGGATAGTC
Statistics
Matches: 332, Mismatches: 31, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
204 331 1.00
205 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (204 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCAGTGTCTCATCA
GGAAGCTAGGGTTCGAAGATTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTAT
CTCATCAGGAAGATGACCGCATCGCTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGACGAA
TTTGGTCCA
Found at i:376551 original size:323 final size:326
Alignment explanation
Indices: 375919--376583 Score: 962
Period size: 323 Copynumber: 2.0 Consensus size: 326
375909 TCACTTTTTT
*** * *
375919 GTATCTCAATCAAGG-AGCTAACTATTTTTATTACTTTGGCTTGCTTCTCAGTATCTCATCAGGA
1 GTATCTC-ATC-AGGAAGCTAACTATTTTTATTACTTCAACATGCTTCTCAGTATCTCACCAGGA
* * *
375983 AGCTGGGGTTCAAAGATTTGCTCATATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCATTATCTC
64 AGCTGGGGTTCAAAGATTTACTCACATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTATCTC
* *
376048 ATCAGGAAGATGACCGCGTCGTTTGTTACAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATT
129 ATCAGGAAGATGACCGCATCGTCTGTTACAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATT
*
376113 TGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACATGCTTCTCGGTGT
194 TGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACATGCTTCTCAGTGT
* * * * * * *
376178 CTTACCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTTCTTC
259 CTCACCAAGAAGCTAGGGTTCAAAGATTTACTCACACCGAGCGCGGGTTTGATTTGGTCTTCTTC
376243 TCA
324 TCA
* * *
376246 GTATCTCATCAGGAAGCTAAC-A-TTTTATTACTTCAACATGCTTCTCGGTGTCTTACCAGGAAG
1 GTATCTCATCAGGAAGCTAACTATTTTTATTACTTCAACATGCTTCTCAGTATCTCACCAGGAAG
* * *
376309 CTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTTTTCTTCTCAGTATCTCAT
66 CTGGGGTTCAAAGATTTACTCACATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTATCTCAT
** * * **
376374 CAGGAAGAT-ATCCGCATCG-CTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGATGAATTT
131 CAGGAAGATGA-CCGCATCGTCTGTTACAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTT
*
376437 GGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTC
195 GGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACATGCTTCTCAGTGTC
* * *
376502 TCATCAAGAAGCTAGGGTTCAAAGATTTGCTCATACCGAGCGCGGGTTTGATTTGGTCTTCTTCT
260 TCACCAAGAAGCTAGGGTTCAAAGATTTACTCACACCGAGCGCGGGTTTGATTTGGTCTTCTTCT
376567 CA
325 CA
376569 GTATCTCATCAGGAA
1 GTATCTCATCAGGAA
376584 AATGACTGCA
Statistics
Matches: 302, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
323 173 0.57
324 108 0.36
325 4 0.01
326 10 0.03
327 7 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (326 bp):
GTATCTCATCAGGAAGCTAACTATTTTTATTACTTCAACATGCTTCTCAGTATCTCACCAGGAAG
CTGGGGTTCAAAGATTTACTCACATCGAGCGCGGGTTTGATTTGGTCTTCTTCTCAGTATCTCAT
CAGGAAGATGACCGCATCGTCTGTTACAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTTG
GTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACATGCTTCTCAGTGTCT
CACCAAGAAGCTAGGGTTCAAAGATTTACTCACACCGAGCGCGGGTTTGATTTGGTCTTCTTCTC
A
Found at i:388292 original size:96 final size:96
Alignment explanation
Indices: 388111--388295 Score: 232
Period size: 96 Copynumber: 1.9 Consensus size: 96
388101 GAAAAGGATG
* ** *
388111 TTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAACTTTGCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTGCAGAATCGA
* *
388176 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTACCTCGATTAAGGGTA
* * *
388207 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTGCAG-AA-TC
*
388271 GAA-ATAAA-AGAATATTACCTCGATT
64 GAAGATAAAGA-AACATTACCTCGATT
388296 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.91
97 5 0.07
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTGCAGAATCGA
AGATAAAGAAACATTACCTCGATTAAGGGTA
Found at i:388641 original size:29 final size:29
Alignment explanation
Indices: 388582--388721 Score: 203
Period size: 30 Copynumber: 4.8 Consensus size: 29
388572 AGACATTCAG
388582 GGTAAAAATGGAATTTTTGGAAGTTTCGA
1 GGTAAAAATGGAATTTTTGGAAGTTTCGA
388611 GGTCAAAAATGGAATTTTTGGAAGTTT-GA
1 GGT-AAAAATGGAATTTTTGGAAGTTTCGA
*
388640 GGGTAAAAATGGAATTTTTGGAAGTTTCGG
1 -GGTAAAAATGGAATTTTTGGAAGTTTCGA
* *
388670 GGTAAAAAATGGAATTTTTGGAAGTTTAGG
1 GGT-AAAAATGGAATTTTTGGAAGTTTCGA
*
388700 GGTAAGAAT-GAATTTTTGGAAG
1 GGTAAAAATGGAATTTTTGGAAG
388722 AATGAAATTT
Statistics
Matches: 104, Mismatches: 3, Indels: 9
0.90 0.03 0.08
Matches are distributed among these distances:
28 13 0.12
29 36 0.35
30 55 0.53
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (29 bp):
GGTAAAAATGGAATTTTTGGAAGTTTCGA
Found at i:388649 original size:59 final size:58
Alignment explanation
Indices: 388580--388922 Score: 305
Period size: 59 Copynumber: 6.1 Consensus size: 58
388570 TTAGACATTC
388580 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTTG
*
388639 AGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAAATGGAATTTTTGGAAGTTT-
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTTG
* * **
388697 AGGGGTAAGAAT-GAATTTTTGG-A------A-G----AATGAAATTTTCAGAAGTTTTG
1 A-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAG-TTTG
* * * *
388744 -GGGTAAAAAATGGAATTTTTGGAAGTATAG-GGTAAAAATGAAAATTTTGGAAGTTTTG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAG-TTTG
* * *
388802 -GGGTCAAAAATGGAATTTTTTGAAG-TTCGAGCGTAAAAATGAAATTTTTTGAAGTTTTG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTCGAG-GTAAAAATGGAATTTTTGGAAG-TTTG
*
388861 -GGGTCAAAAATTG-ATTCTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCG
1 AGGGT-AAAAATGGAATT-TTTGGAAGTTTCGA-GGTAAAAATGGAATTTTTGGAAGTTT-G
388920 AGG
1 AGG
388923 TCTTTTGGGC
Statistics
Matches: 240, Mismatches: 21, Indels: 45
0.78 0.07 0.15
Matches are distributed among these distances:
45 18 0.08
46 8 0.03
47 10 0.04
48 1 0.00
50 1 0.00
54 1 0.00
57 3 0.01
58 60 0.25
59 135 0.56
60 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTTG
Found at i:388789 original size:29 final size:28
Alignment explanation
Indices: 388744--388916 Score: 138
Period size: 29 Copynumber: 6.0 Consensus size: 28
388734 AGAAGTTTTG
*
388744 GGGTAAAAAATGGAATTTTTGGAAGTATA
1 GGGTCAAAAATGGAATTTTTGGAAGT-TA
* * *
388773 GGGT-AAAAATGAAAATTTTGGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTGGAAG--TTA
*
388802 GGGTCAAAAATGGAATTTTTTGAAGTTCGA
1 GGGTCAAAAATGGAATTTTTGGAAGTT--A
* * * *
388832 GCGT-AAAAATGAAATTTTTTGAAGTTTTG
1 GGGTCAAAAATGGAATTTTTGGAAG--TTA
*
388861 GGGTCAAAAATTG-ATTCTTTGGAAGTTCGA
1 GGGTCAAAAATGGAATT-TTTGGAAGTT--A
388891 GGGT-AAAAATGGAATTTTTGGAAGTT
1 GGGTCAAAAATGGAATTTTTGGAAGTT
388917 TCGAGGTCTT
Statistics
Matches: 116, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
28 22 0.19
29 51 0.44
30 41 0.35
31 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (28 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTA
Done.