Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009946.1 Corchorus capsularis cultivar CVL-1 contig09967, 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: 55569
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:10580 original size:18 final size:18
Alignment explanation
Indices: 10528--10582 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
10518 TTGTTTGTGT
* *
10528 AGAGGCTGATTGAAAAAG
1 AGAGGTTGATTGAAAAGG
10546 AGAGGTTGATTGAAAAGG
1 AGAGGTTGATTGAAAAGG
10564 AGAGGTTGATTGAAAAGG
1 AGAGGTTGATTGAAAAGG
10582 A
1 A
10583 TTTCGTGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.42, C:0.02, G:0.36, T:0.20
Consensus pattern (18 bp):
AGAGGTTGATTGAAAAGG
Found at i:11447 original size:78 final size:78
Alignment explanation
Indices: 11324--11481 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
11314 GAAAGGACGA
11324 GGAGGACTACTCTTTGCTGCACATGCATTACATCTACATCCAAAAAAATGATGAGTTGCTTCTTG
1 GGAGGACTACTCTTTGCTGCACATGCATTACATCTACATCCAAAAAAATGATGAGTTGCTTCTTG
11389 AGACGGTGGTGAT
66 AGACGGTGGTGAT
* *
11402 GGAGGACTAGTCTTTGCTGCACATGCATTGCATCTACATCCAAAAAAATGATGAGTTGCTTCTTG
1 GGAGGACTACTCTTTGCTGCACATGCATTACATCTACATCCAAAAAAATGATGAGTTGCTTCTTG
11467 AGACGGTGGTGAT
66 AGACGGTGGTGAT
11480 GG
1 GG
11482 TTGGCGAAAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (78 bp):
GGAGGACTACTCTTTGCTGCACATGCATTACATCTACATCCAAAAAAATGATGAGTTGCTTCTTG
AGACGGTGGTGAT
Found at i:16972 original size:3 final size:3
Alignment explanation
Indices: 16964--17017 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
16954 TCATATTCAA
16964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17012 AAT AAT
1 AAT AAT
17018 GTATCCATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:26451 original size:31 final size:31
Alignment explanation
Indices: 26394--26460 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
26384 CAATTTGGGT
*
26394 CTAAACCTTTTAAAAGTTGCCTAATTTGAAC
1 CTAAACCTTTAAAAAGTTGCCTAATTTGAAC
*
26425 CTAAACCTTTCAAAAAG-TGACC-AATTTGAGC
1 CTAAACCTTT-AAAAAGTTG-CCTAATTTGAAC
26456 CTAAA
1 CTAAA
26461 AGTAGAAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (31 bp):
CTAAACCTTTAAAAAGTTGCCTAATTTGAAC
Found at i:27234 original size:26 final size:26
Alignment explanation
Indices: 27198--27248 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
27188 TCTGTCAGGG
27198 ATTTTTTCACTATTCAAACACGAAAC
1 ATTTTTTCACTATTCAAACACGAAAC
27224 ATTTTTTCACTATTCAAACACGAAA
1 ATTTTTTCACTATTCAAACACGAAA
27249 ACCTTACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (26 bp):
ATTTTTTCACTATTCAAACACGAAAC
Found at i:30064 original size:437 final size:438
Alignment explanation
Indices: 29272--30150 Score: 1114
Period size: 437 Copynumber: 2.0 Consensus size: 438
29262 AATAGTTTTA
* * * *
29272 TTGGATTATTTATCTAATGATCCTCATACTTTTATACTTTATGCTATTTAGTCCTTTACAATTAT
1 TTGGATTATTTATCAAATGACCCTCATACTTTTATACTTTATACTACTTAGTCCTTTACAATTAT
* * * *
29337 AGGTTGGACGATTTAACGCGTTGGCTTTTATTTTTGTATTTTTTTTCTATTTGTCCGATTAAGCT
66 AGCTT-GAC-ATCTAACGCGTTAGCTTTTATTTTTGTATTTTTGTTCTATTTGTCCGATTAAGCT
**
29402 GATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCATTAAGAACTCAAAAACCAA
129 GATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCAAGAAGAACTCAAAAACCAA
* * * * *
29467 TTTTAATGTGTTGATTCTAAAAAATGGTTCCGAAATTTTGTGGTTTTGATTGCCGATTAATTTAA
194 TTTTAATGTGTTAATTCAAAAAAATGCTTCCGAAATTTGGTGGTTTCGATTGCCGATTAATTTAA
* * * ** * * *
29532 TATCGTATAATTTTTTGTCCACATGTCTGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTG
259 TATCATATAATCTTTCGTCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTG
* * * *
29597 CATGATTTACGACTTTCATGAAGGACCCGAAAGCTAAATTTGATCTACGAGTTTCGTTAAGGGTT
324 CATGATCTACGACTTTCATGAAGAACCCGAAAG-TAAATTTGATCTACGAGTTTCATGAAGGGTT
29662 -AAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTAT
388 CAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTAT
* *
29712 TTGGATTATTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAGTCCTTTACAAATTC
1 TTGGATTATTTATCAAATGACCCTCATACTTTTATACTTTATACTACTTAGTCCTTTAC-AATTA
* * * * *
29777 TATCTT-A-ATCTGACG-TTTAAGC-TTTATTTTTTTATTCTTTGTTCTATTTGTCCGATTAAGT
65 TAGCTTGACATCTAACGCGTT-AGCTTTTATTTTTGTATT-TTTGTTCTATTTGTCCGATTAAGC
* * * **
29838 TGATTCATGTGTCTATTAAAAGGTAATTTCATGATTTACAACTTTT-AAGAAGGACTC-AAAAGT
128 TGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAA-TTTTCAAGAAGAACTCAAAAACC
* * ** *
29901 AATTTTTTATGT-TTCAATTCAAAAAAATGCTT-CGTAAATTTGGTTGTTTCGATTGTTGGTCT-
192 AA-TTTTAATGTGTT-AATTCAAAAAAATGCTTCCG-AAATTTGGTGGTTTCGATTGCCGAT-TA
*
29963 ATTTAATATCATATAA-CTTTCGATCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTGAAAG
253 ATTTAATATCATATAATCTTTCG-TCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAG
* * * *
30027 GTTACTGTATGGTCTACGACTTTCATGAAGAACCCGAAAGTTAATTTGATCTACGAGTTTCATGG
317 GTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAGTAAATTTGATCTACGAGTTTCATGA
**
30092 AGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAATTATTTTCTTAT
382 AGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTAT
30149 TT
1 TT
30151 TTTTACTCGA
Statistics
Matches: 378, Mismatches: 51, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
436 56 0.15
437 254 0.67
438 5 0.01
439 1 0.00
440 54 0.14
441 8 0.02
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (438 bp):
TTGGATTATTTATCAAATGACCCTCATACTTTTATACTTTATACTACTTAGTCCTTTACAATTAT
AGCTTGACATCTAACGCGTTAGCTTTTATTTTTGTATTTTTGTTCTATTTGTCCGATTAAGCTGA
TTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAATTTTCAAGAAGAACTCAAAAACCAATT
TTAATGTGTTAATTCAAAAAAATGCTTCCGAAATTTGGTGGTTTCGATTGCCGATTAATTTAATA
TCATATAATCTTTCGTCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCA
TGATCTACGACTTTCATGAAGAACCCGAAAGTAAATTTGATCTACGAGTTTCATGAAGGGTTCAA
AAGGGAATTTTTATGTTTCAAGATCTCCATTAACAAACATTTTCTTAT
Found at i:38127 original size:20 final size:20
Alignment explanation
Indices: 38102--38139 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38092 CTTTTAAATT
*
38102 AAAAAAAAAGGAATAAAACG
1 AAAAAAAAAGGAAGAAAACG
38122 AAAAAAAAAGGAAGAAAA
1 AAAAAAAAAGGAAGAAAA
38140 AGCCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAGGAAGAAAACG
Found at i:50471 original size:19 final size:21
Alignment explanation
Indices: 50433--50472 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50423 ACTCATAATC
*
50433 TCTATTTATTTTTTATTATAT
1 TCTATTTATTTTTCATTATAT
50454 TCTATTT-TTTTTCA-TATAT
1 TCTATTTATTTTTCATTATAT
50473 GATACTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTATTTATTTTTCATTATAT
Found at i:50556 original size:17 final size:18
Alignment explanation
Indices: 50534--50568 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
50524 CTATTTTTAA
50534 AATTGTTAATT-TTAATT
1 AATTGTTAATTGTTAATT
50551 AATTGTTAATTGTTAATT
1 AATTGTTAATTGTTAATT
50569 TTTATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
AATTGTTAATTGTTAATT
Found at i:51573 original size:333 final size:330
Alignment explanation
Indices: 50771--53643 Score: 2510
Period size: 331 Copynumber: 8.5 Consensus size: 330
50761 AAACAGAGCC
* * * * * * * *
50771 TAAATCGAAACAAGATTCAGATGCACGTAAAGAGAAATCCTTAAATCCAATGTGGATGAAATTAG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * * *
50836 ATTAGATGAATAAAGATATTTCAAGGAGTC--TCGGCACCAAAAATCATGCAAAACAGAGCCTTG
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCA--AAAAATCATGCAAAACTGAGTC-GG
* * * * *
50899 ACCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAA-A--G-
128 GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGC
* * * * * *
50960 ----A--GACCCGAAACGTTTTTTTCTCAAATTTTAGCCACAATACTAATATATATATATATGTA
193 AAAAACTGACCCGAAATG-TTTTTCCTCAATTTTTTGCCACAATACT--CAGA-A-A-A-A---A
* ** **
51019 TATATAATTCAACG-CAAAAAGATT-AACGGGCTTTTCACGCTTCTAATATAATTTTTCCATTTT
248 TATATAATTCAACGCCAAAAAAATTGAA-GGATTTTTCACGCTTCTAATATGTTTTTTCCATTTT
* *
51082 TTTCGAATTAATTT-TTAT
312 TTTCGAATTTATTTCTAAT
* * * ** * * * *
51100 CAAATCGAAAAAAGATTCAGATGCTCAAAAAAATAAATCCTTATATCCAATGTGGCTGAAATTTG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * *
51165 GTTCGATGAATATAGATATTTCAAAGAGTTTTTGC-GCAAAAAAT-ATGCAAAATTGAGCCGGCG
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCAAAAAATCATGCAAAACTGAGTCGG-G
* * * * * *
51228 CACCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTCAGTACACGATTTCGGTTAAAATTTTGCA
129 CCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGCA
*
51293 AAAACTGACCCGAAATGTTTTTCCTCAATTTTTTACCACAATACTCA-AAAAAATATATAATTCA
194 AAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCA
* * * *
51357 ATGCCAAAAAATTTGAAGGGTTTTTCACACTTCTAATATTGTTTTTTCCATTTTTTTTCCTGAAT
259 ACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATA-TGTTTTTTCCA-TTTTTTT-C-GAAT
*
51422 TTATTTCAAAT
320 TTATTTCTAAT
* * *
51433 TAAACCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * *
51498 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCAGTAAAAAATCATGGAAAACTGTGACGGGCC
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAGTCGGGCC
* * * * *
51563 CCGAAACGCGTTTTTAGTCAAAATCCATGATGGTTAGTACATGAA-TTCGGGTAAAA-ACTTGCA
131 CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA-CAATTTCGGCTAAAATA-TTGC-
* *
51626 AAACTGAATTGAGACCCCGAAACTCGTTTTTAGCCATAAACCGTGATTTTTAGTACACGATTTCG
193 AAA---AACT--GA-CCCGAAA-T-GTTTTT--CC-TCAA---T--TTTTT-G--C-C-A-----
* * * ** * **
51691 GCTAAAAACTGACAAGAAAAATATTTCTTTAATTTTTTTCGACAATACTCAGAAAAAA--AAAAT
232 -C--AATACT--C-AGAAAAA-A--TATATAA-----TT---CAACGC-CA-AAAAAATTGAAGG
** *
51754 ATAATTCAACGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCG-TTTTCCCATTTTTT
278 ATTTTTC-ACG---------------------------CTTCTAATAT-GTTTTTTCCATTTTTT
*
51818 TCCAATTTATTTCTAAT
314 TCGAATTTATTTCTAAT
* * * * *
51835 TAAATCGAAACAAGATTCAGGTGCTCGCAAAACCAAGTCCTTAAATACATTGTGGCTGAGATTTA
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * *
51900 G-TAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAGCTTGCACAACTGAGTCGAGAC
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAGTCG-GGC
* * *
51964 CCCGAAACCCGTTTTTAGCCAAAAACCGTTAT-GTAACGTACACAATTTTCGGC--------T--
130 CCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACAA-TTTCGGCTAAAATATTGC
* * * *
52018 AAAAACTGACCCAAAATTTTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAAATTATATAA
193 AAAAACTGACCCGAAA-TGTTTTTCCTCAATTTTTTGCCACAATACTCAG-AAAAAA-TATATAA
* * * ***
52083 TTCAACTCCAAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTCTTTTTTTTTTTTCG
255 TTCAACGCC-AAAAAAATTGAAGGATTTTTCACGCTTCTAATAT-GTTTT-TTCCATTTTTTTCG
*
52148 AATTTATTTATAAT
317 AATTTATTTCTAAT
* *
52162 TAAATTGAAACGAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATT-TCGGCTGAGATTT
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGT-GGCTGAGATTT
* * *
52226 GGTTAGATGAATATAGATATTTC-ACGAGTCTTTCAGCCAAAAAATCATGCAAAACTGAGTTGGG
65 GGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTG-CAAAAAATCATGCAAAACTGAG-TCGG
* ** *
52290 GCCTCGAAACGTATTTTTAGCAAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGC
128 GCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGC
* * ** *
52355 AAAAACTGACCCGAAAAT-TTTTTTCTCAAATTTTTGCCACAATAAACAGGAAAAATATATAATT
193 AAAAACTGACCCG-AAATGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
* *
52419 CAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCTTTTTT-CATTTTTTTTTGAATT
257 CAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATGTTTTTTCCA-TTTTTTTCGAATT
*
52483 TATCTCTAAT
321 TATTTCTAAT
52493 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * * *
52558 GTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGC-AAAAATCATGCGAAACTGAGTTGGGGC
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAG-TCGGGC
* * * * *
52622 CTCGAAACGCGTTTTTAGCCAAAAACCATTATGGTTATTACACAATTTCGGCTAAAATATTACAA
130 CCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGCAA
** * *
52687 AAACAAACCCGAAAATTTTTTTCCTCAA-TTTTTGCCACAATACTCAGGAAAACATATATAATTC
195 AAACTGACCCG-AAATGTTTTTCCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAATTC
* * * * ** *
52751 AAC-ACAAAAAAAATGAAGGGTTTTTCATGCTTCTAATATCATTTTTCCATTTTTTTCCAAATTT
258 AACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATGTTTTTTCCATTTTTTT-CGAATTT
*
52815 ATCTCTAAT
322 ATTTCTAAT
* * *
52824 TAAATCGAAACAAGATTCAGGTGCTCGTAAATACAAATCCTTAAATCCATTGTGACTGAAATTTG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * * *
52889 GTTTGATGAGTATAGATATTCCAAGGTGTCTTTCTGCCAAAAAATCATGCAAAACTGAGTCGGAG
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTG-CAAAAAATCATGCAAAACTGAGTCGG-G
* * * *
52954 CCCCGAAACGCGTTTTTAGCTAAAAACCGTGATGATTAGTACACAATTTCGGCTAAACTATTGTA
129 CCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGCA
* ** *
53019 AAAACTGACCCGAAAAT-TTTATCCTCAATTTTTTGCCACAATAAACATAAAAGAATATATAATT
194 AAAACTGACCCG-AAATGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAA-AATATATAATT
53083 CAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCG-TTTTTCCATTTTTTTCGAATT
257 CAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATAT-GTTTTTTCCATTTTTTTCGAATT
*
53147 TATTTATAAT
321 TATTTCTAAT
* * * * * *
53157 TAAATCGAAACGAGATTCAGGTGTTCGTAAAAACAAATCCTTAAATTCATTGCGGCTAATATTTG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * *
53222 GTAAGATGAATATAGATATTTCACGGAGTCTTTCAGCCAAAAAATCATGCAAAACTGAGTCGGGG
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTG-CAAAAAATCATGCAAAACTGAGTC-GGG
* * * * * *
53287 CCTCGAAACGCATTTTTAGCC-AAAGCAGTGATGGTTAGTATACAATTTCGGCTAAAATATTACA
129 CCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGCA
**
53351 AAAACTGACCCGAAA-GTTTTTCCTCAATTTTTTGCCACAATAAACAGAAAAACATATATAATTC
194 AAAACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTC
* ** *
53415 AACACCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCATTTTTCCATTTTATTCGAATTTA
258 AACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATGTTTTTTCCATTTTTTTCGAATTTA
*
53480 TCTCTAAT
323 TTTCTAAT
* *
53488 TAAATCGAAACAAGATTCAGGTGCTCGTAAATACAAATCCTTAATTCCATTGTGGCTGAGATTTG
1 TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
* * ** * ** *
53553 GTTAGATGAAAATAGATATTCCAAGGACACTTTTTGC-AAAAATCATGTGAAACTGAGCCGGGGC
66 GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAGTC-GGGC
* * *
53617 CCCTAAACGCGTGTTTAGCGAAAAACC
130 CCCGAAACGCGTTTTTAGCCAAAAACC
53644 ATATATAATT
Statistics
Matches: 2098, Mismatches: 300, Indels: 291
0.78 0.11 0.11
Matches are distributed among these distances:
325 12 0.01
326 4 0.00
327 112 0.05
328 167 0.08
329 141 0.07
330 173 0.08
331 446 0.21
332 92 0.04
333 444 0.21
334 82 0.04
335 7 0.00
336 26 0.01
337 40 0.02
338 13 0.01
339 2 0.00
340 7 0.00
341 1 0.00
342 6 0.00
344 2 0.00
345 3 0.00
348 1 0.00
350 5 0.00
351 7 0.00
352 7 0.00
353 7 0.00
354 1 0.00
355 3 0.00
360 6 0.00
361 4 0.00
362 5 0.00
363 5 0.00
364 5 0.00
365 1 0.00
366 2 0.00
367 5 0.00
368 1 0.00
370 5 0.00
372 1 0.00
373 1 0.00
374 1 0.00
375 2 0.00
376 1 0.00
377 4 0.00
378 11 0.01
379 5 0.00
380 5 0.00
382 3 0.00
383 2 0.00
385 5 0.00
386 7 0.00
387 2 0.00
389 3 0.00
392 3 0.00
395 1 0.00
401 55 0.03
402 105 0.05
403 6 0.00
404 7 0.00
405 8 0.00
406 10 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (330 bp):
TAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTG
GTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAGTCGGGCC
CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGCAAA
AACTGACCCGAAATGTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC
GCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATGTTTTTTCCATTTTTTTCGAATTTATTT
CTAAT
Found at i:53410 original size:664 final size:662
Alignment explanation
Indices: 51745--53643 Score: 2582
Period size: 664 Copynumber: 2.9 Consensus size: 662
51735 ATACTCAGAA
* * *
51745 AAAAAAAATATAATTCAACGCCAAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCC
1 AAAAAATATATAATTCAACGCC-AAAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTC
* * * *
51810 CATTTTTTTCCAATTTATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGCAAAACCAAGTCC
65 CATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCC
*
51875 TTAAATACATTGTGGCTGAGATTTAGTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAA
130 TTAAATACATTGTGGCTGAGATTTGGTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAA
* * * * * * * * *
51940 AAGCTTGCACAACTGAGTCGAGACCCCGAAACCCGTTTTTAGCCAAAAACCGTTAT-GTAACGTA
195 AATCATGCAAAACTGAGTCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACAGTTATGGTTA-GTA
* *
52004 CACAATTTTCGGC--------T--AAAAACTGACCCAAAATTTTTTTTCCTCAATTCTTTGCCAC
259 CACAA-TTTCGGCTAAAATATTACAAAAACTGACCCGAAA-TTTTTTTCCTCAATTTTTTGCCAC
* * *
52059 AATACTA-AGAAAAAAATTATATAATTCAACTCCAAAAAAAATTGAAGGGTTTTTCATGCTTCTA
322 AATA-AACAGAAAAACA-TATATAATTCAAC-ACAAAAAAAA-TGAAGGGTTTTTCATGCTTCTA
* *** * * * *
52123 ATATCGTTTTCTTTTTTTTTTTTCGAATTTATTTATAATTAAATTGAAACGAGATTCAGGTGCTC
383 ATATC-ATTT-TTCCATTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTC
* * *
52188 GTAAAAACAAATCCTTAAATCCATT-TCGGCTGAGATTTGGTTAGATGAATATAGATATTTC-AC
446 GTAAATACAAATCCTTAAATCCATTGT-GGCTGAGATTTGGTTAGATGAATATAGATATTCCAAG
* * * **
52251 GAGTCTTTCAGCCAAAAAATCATGCAAAACTGAGTTGGGGCCTCGAAACGTATTTTTAGCAAAAA
510 GAGTCTTTCTGCCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAA
* * *
52316 ACCGTGATGGTTAGTACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTTTTCT
575 ACCGTGATGATTAGTACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTATCCT
52381 CAAATTTTTGCCACAATAAACAG
640 CAAATTTTTGCCACAATAAACAG
* *
52404 GAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATC-TTTTTTC
1 AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCC
* *
52468 ATTTTTTTTTGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCC
66 A-TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCC
* * * *
52533 TTAAATCCATTGTGGCTGAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTG-CAA
130 TTAAATACATTGTGGCTGAGATTTGG-TAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAA
* * *
52597 AAATCATGCGAAACTGAGTTGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCA-TTATGGTTATT
194 AAATCATGCAAAACTGAGTCGGGGCCTCGAAACGCGTTTTTAGCCAAAAA-CAGTTATGGTTAGT
**
52661 ACACAATTTCGGCTAAAATATTACAAAAACAAACCCGAAAATTTTTTTCCTCAA-TTTTTGCCAC
258 ACACAATTTCGGCTAAAATATTACAAAAACTGACCCG-AAATTTTTTTCCTCAATTTTTTGCCAC
** *
52725 AATACTCAGGAAAACATATATAATTCAACACAAAAAAAATGAAGGGTTTTTCATGCTTCTAATAT
322 AATAAACAGAAAAACATATATAATTCAACACAAAAAAAATGAAGGGTTTTTCATGCTTCTAATAT
*
52790 CATTTTTCCATTTTTTTCCAAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAA
387 CATTTTTCCATTTTTTT-CGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAA
* * * * *
52855 TACAAATCCTTAAATCCATTGTGACTGAAATTTGGTTTGATGAGTATAGATATTCCAAGGTGTCT
451 TACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTCCAAGGAGTCT
* *
52920 TTCTGCCAAAAAATCATGCAAAACTGAGTCGGAGCCCCGAAACGCGTTTTTAGCTAAAAACCGTG
516 TTCTGCCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTG
* * *
52985 ATGATTAGTACACAATTTCGGCTAAACTATTGTAAAAACTGACCCGAAAATTTTATCCTCAATTT
581 ATGATTAGTACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTATCCTCAAATT
*
53050 TTTGCCACAATAAACAT
646 TTTGCCACAATAAACAG
53067 AAAAGAATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTC
1 AAAA-AATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTC
* * *
53132 CATTTTTTTCGAATTTATTTATAATTAAATCGAAACGAGATTCAGGTGTTCGTAAAAACAAATCC
65 CATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCC
* * * * * *
53197 TTAAATTCATTGCGGCTAATATTTGGTAAGATGAATATAGATATTTCACGGAGTCTTTCAGCCAA
130 TTAAATACATTGTGGCTGAGATTTGGT-AGATGAATATAGATATTTCAAGGAGTCTTTCTGCC-A
* * *
53262 AAAATCATGCAAAACTGAGTCGGGGCCTCGAAACGCATTTTTAGCC-AAAGCAGTGATGGTTAGT
193 AAAATCATGCAAAACTGAGTCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACAGTTATGGTTAGT
* *
53326 ATACAATTTCGGCTAAAATATTACAAAAACTGACCCGAAA-GTTTTTCCTCAATTTTTTGCCACA
258 ACACAATTTCGGCTAAAATATTACAAAAACTGACCCGAAATTTTTTTCCTCAATTTTTTGCCACA
* * *
53390 ATAAACAGAAAAACATATATAATTCAACACCAAAAAAATTGAAGGATTTTTCACGCTTCTAATAT
323 ATAAACAGAAAAACATATATAATTCAACA-CAAAAAAAATGAAGGGTTTTTCATGCTTCTAATAT
*
53455 CATTTTTCCATTTTATTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAT
387 CATTTTTCCATTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAT
* * **
53520 ACAAATCCTTAATTCCATTGTGGCTGAGATTTGGTTAGATGAAAATAGATATTCCAAGGACACTT
452 ACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTT
* ** * * * *
53585 TTTG-C-AAAAATCATGTGAAACTGAGCCGGGGCCCCTAAACGCGTGTTTAGCGAAAAACC
517 TCTGCCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACC
53644 ATATATAATT
Statistics
Matches: 1094, Mismatches: 119, Indels: 51
0.87 0.09 0.04
Matches are distributed among these distances:
657 13 0.01
658 170 0.16
659 55 0.05
661 9 0.01
662 140 0.13
663 183 0.17
664 318 0.29
665 116 0.11
666 64 0.06
667 23 0.02
668 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (662 bp):
AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCGTTTTTCC
ATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCT
TAAATACATTGTGGCTGAGATTTGGTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
ATCATGCAAAACTGAGTCGGGGCCTCGAAACGCGTTTTTAGCCAAAAACAGTTATGGTTAGTACA
CAATTTCGGCTAAAATATTACAAAAACTGACCCGAAATTTTTTTCCTCAATTTTTTGCCACAATA
AACAGAAAAACATATATAATTCAACACAAAAAAAATGAAGGGTTTTTCATGCTTCTAATATCATT
TTTCCATTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAATACAA
ATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTCTG
CCAAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGAT
TAGTACACAATTTCGGCTAAAATATTGCAAAAACTGACCCGAAAATTTTATCCTCAAATTTTTGC
CACAATAAACAG
Found at i:54282 original size:572 final size:569
Alignment explanation
Indices: 53134--54223 Score: 1405
Period size: 572 Copynumber: 1.9 Consensus size: 569
53124 CGTTTTTCCA
* * * * *
53134 TTTTTTTCGAATTTATTTATAATTAAATCGAAACGAGATTCAGGTGTTCGTAAAAACAAATCCTT
1 TTTTTTTCGAATTTATCTACAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCAT
* * *
53199 AAATTCATTGCGGCTAATATTTGGTAAGATGAATATAGATATTTCACGGAGTCTTTCAGCCAAAA
66 AAATCCATTGCGACTAATATTTGGTAAGATGAATATAGATATTTCAAGGAGTCTTTCAGCCAAAA
* * *
53264 AATCATGCAAAACTGAGTCGGGGCCTCGAAACGCATTTTTAGCCAAAGCAGTGATGGTTAGTATA
131 AATCATGCAAAACTGAGTCGGGGCCTCAAAACGCATTTTTAGCAAAAGCAGTGATGGTTAGTACA
**
53329 CAATTTCGGCTAAAATATTACAAAAACTGACCCGAAAGTTTTTCCTCAATTTTTTGCCACAATAA
196 CAATTTCGGCTAAAATATTACAAAAACAAACCCGAAAGTTTTTCCTCAATTTTTTGCCACAATAA
53394 ACAGAAAAACATATATAATTCAACACCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCATT
261 ACAGAAAAACATATATAATTCAACACCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCATT
* *
53459 TTTCCATTTTATTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAATACAA
326 TTTCCATTTTATTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAA
* ** * *
53524 ATCCTTAATTCCATTGTGGCTGAGATTTGGTTAGATGAAAATAGATATTCCAAGGACACTTTTTG
391 ATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAAAATAGATATTCCAAGGACACTTTCTG
** * ** ** * *
53589 CAAAAATCATGTGAAACTGAGCCGGGGCCCCTAAACGCGTGTTTAGCGAAAAACCATATATAATT
456 CAAAAATCATGCAAAACTAAGAAGGACCCCCAAAACGCGTGTTTAGCGAAAAACCATAGATAATT
* * *** * * ***
53654 CAACACCAAAAAAATTGAAGAGTTTTTCATGCTTCTAATATCATTTTTCAAT
521 CAACACC--AAAAATT-AACAGTCTAAAATGATTCTAATATAATTACCCAAT
* * *
53706 TTTTTTTCGAATTTATCTCCAATTAAATCGAAACAAGATTCAGGTGCTCGTAAATACAGATCCAT
1 TTTTTTTCGAATTTATCTACAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCAT
** * * *
53771 AAATCCATTTTGACTGAA-ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCTAAA
66 AAATCCATTGCGACT-AATATTTGGTAAGATGAATATAGATATTTCAAGGAGTCTTTCAGCCAAA
* * *
53835 AAATCATGCAAAACTGAGTCGGGGCAC-CAAAACGCGTTTTTGGCTAAAAATCA-TGATGGTTAG
130 AAATCATGCAAAACTGAGTCGGGGC-CTCAAAACGCATTTTTAGC--AAAAGCAGTGATGGTTAG
* * * *
53898 TACACAATTTCGGCTAAAATGTTGCAAAAACAAACCCGAAAATTTTTTCCTCCATTTTTTGCCAC
192 TACACAATTTCGGCTAAAATATTACAAAAACAAACCCG-AAAGTTTTTCCTCAATTTTTTGCCAC
** * *
53963 AATACTCAGAAAAACATATATAATTCAACACC-AAAAAATTGAAGGGTTTTTCATGCTTCTAATA
256 AATAAACAGAAAAACATATATAATTCAACACCAAAAAAATTGAAGGATTTTTCACGCTTCTAATA
*
54027 TCATTTTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCG
321 TCATTTTTCCA---TTT-TATTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCG
* * *
54092 TAAAAACAAATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGT
382 TAAAAACAAATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAAAATAGATATTCCAAGGA
** * * * *
54157 GTCTTTCTGCCGAAAAATCATGCAAAACTAAGTAAGGACCCCCAAAACTCGTTTTTGGCTAAAAA
447 CACTTTCTG-C-AAAAATCATGCAAAACTAAG-AAGGACCCCCAAAACGCGTGTTTAGCGAAAAA
54222 CC
509 CC
54224 GTGATGGTTA
Statistics
Matches: 449, Mismatches: 57, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
572 149 0.33
573 87 0.19
574 59 0.13
576 3 0.01
577 108 0.24
578 1 0.00
579 17 0.04
580 25 0.06
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (569 bp):
TTTTTTTCGAATTTATCTACAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCAT
AAATCCATTGCGACTAATATTTGGTAAGATGAATATAGATATTTCAAGGAGTCTTTCAGCCAAAA
AATCATGCAAAACTGAGTCGGGGCCTCAAAACGCATTTTTAGCAAAAGCAGTGATGGTTAGTACA
CAATTTCGGCTAAAATATTACAAAAACAAACCCGAAAGTTTTTCCTCAATTTTTTGCCACAATAA
ACAGAAAAACATATATAATTCAACACCAAAAAAATTGAAGGATTTTTCACGCTTCTAATATCATT
TTTCCATTTTATTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAA
ATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAAAATAGATATTCCAAGGACACTTTCTG
CAAAAATCATGCAAAACTAAGAAGGACCCCCAAAACGCGTGTTTAGCGAAAAACCATAGATAATT
CAACACCAAAAATTAACAGTCTAAAATGATTCTAATATAATTACCCAAT
Found at i:55107 original size:666 final size:661
Alignment explanation
Indices: 53644--55569 Score: 2880
Period size: 666 Copynumber: 2.9 Consensus size: 661
53634 GCGAAAAACC
* * * *
53644 ATATATAATTCAACACCAAAAAAATTGAAGAGTTTTTCATGCTTCTAATATCATTTTTCAATTTT
1 ATATATAATTCAACGCCAAAAAAATTGAAGA-TTTTTCACGCTTCTAATATCGTTTTTCCA-TTT
* * * * *
53709 TTTTCGAATTTATCTCCAATTAAATCGAAACAAGATTCA-GGTGCTCGTAAATACAGATCCATAA
64 TTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCATGG-GCTTGTAAAAACAAATCCTTAA
* * * * * * *
53773 ATCCATTTTGACTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCTAAAAAA
128 ATCCATTGTGGCTTAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGC--AAAAA
* * * * *
53838 TCATGCAAAACTGAGTC-GGGGCACCAAAACGCGTTTTTGGCTAAAAATCATGATGGTTAGTACA
191 TCATGCAAAACAGAG-CAGGGGC-CCGAAACGCGTTTTTAGC-AAAAA-CGTGATGGTTAATACA
* * *
53902 CAATTTCGGCTAAAATGTTGCAAAAACAAACCCGAAAATTTTTTCCTCCATTTTTTGCCACAATA
252 CAATTTCGGCTAAAATATTGCAGAAACAAATCCGAAAATTTTTTCCTCCATTTTTTGCCACAATA
53967 CTCAGAAAAACATATATAATTCAACACCAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATT
317 CTCAGAAAAACATATATAATTCAACACCAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATT
54032 TTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAA
382 TTTCCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAA
54097 ACAAATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTT
447 ACAAATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTT
**
54162 TCTGCCGAAAAATCATGCAAAACTAAGTAAGGACCCCCAAAACTCGTTTTTGGCTAAAAACCGTG
512 TCTGCCGAAAAATCATGCAAAACTAAGT--GG-GGCCCAAAACTCGTTTTTGGCTAAAAACCGTG
* * *
54227 ATGGTTAGTACACAATTTCAGCTAAAATATTGTAAAAATTGACCCGAAAATTTTTTCATCAACTT
574 ATGGTTAGTACACAATTTCAGCTAAAATATTGCAAAAACTGAACCGAAAATTTTTTCATCAACTT
**
54292 TTTGTTACAATAAACAGAAAAAA
639 TTTGCCACAATAAACAGAAAAAA
* * * *
54315 ATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTAACACTTCTAAAATCGTTTTCCCATTTT
1 ATATATAATTCAACGCCAAAAAAATTGAA-GATTTTTCACGCTTCTAATATCGTTTTTCCATTTT
*
54380 TTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCATGGACTTGTAAAAACAAATCCTTAAAT
65 TTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCATGGGCTTGTAAAAACAAATCCTTAAAT
* *
54445 CCAATGTGGCTTAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGCCAAAATCAT
130 CCATTGTGGCTTAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGCAAAAATCAT
* * *
54510 GCAAAACAGAGCAGGGGCCCGAAACACGGTTTTAGCCAAAACGGTGATGGTTAATACACAATTTC
195 GCAAAACAGAGCAGGGGCCCGAAACGCGTTTTTAGCAAAAAC-GTGATGGTTAATACACAATTTC
*
54575 GGCTAAAATATTGCAGAAACAAATTCCGAAATTTTTTTCCTCCATTTTTTGCCACAATACTCAGA
259 GGCTAAAATATTGCAGAAACAAA-TCCGAAAATTTTTTCCTCCATTTTTTGCCACAATACTCAGA
*
54640 AAAACATATATAATTCAACACCAAAAATATTGAAAGGTTTTTCATGCTTCTAATATCATTTTTCC
323 AAAACATATATAATTCAACACCAAAAA-ATTGAAGGGTTTTTCATGCTTCTAATATCATTTTTCC
54705 ATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAA
387 ATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAA
** * *
54770 TCCTTAAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
452 TCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTTTCTGC
* * *
54835 CGAAAAATCATGCAAAACTGAGTCGGGGCCCGAAA-TGCGTTTTTGGCTAAAAACTGTGATGGTT
517 CGAAAAATCATGCAAAACTAAGT-GGGGCCCAAAACT-CGTTTTTGGCTAAAAACCGTGATGGTT
* * *
54899 AGTACACAATTTCGGCTAAAATATTGCAAAAACTGAACCGAAAATTTTTTTCCTCAATTTTTTGC
580 AGTACACAATTTCAGCTAAAATATTGCAAAAACTGAACCGAAAA-TTTTTTCATCAACTTTTTGC
54964 CACAATAAACAG-AAAAA
644 CACAATAAACAGAAAAAA
54981 ATATATAATTCAACGCCAAAAAAATTGAAGTATTTTTCACGCTTCTAATATCGTTTTTCCATTTT
1 ATATATAATTCAACGCCAAAAAAATTGAAG-ATTTTTCACGCTTCTAATATCGTTTTTCCATTTT
*
55046 TTTCGAATTTATCTCTAATTAAATCGAAACAAAATTCATGGGCTTGTAAAAACAAATCCTTAAAT
65 TTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCATGGGCTTGTAAAAACAAATCCTTAAAT
*
55111 CCATTGTGGCTTAGATTTGATTAGATGAAAATAGATATTTCAAGGAGACTTTTTGCAAAAATCAT
130 CCATTGTGGCTTAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGCAAAAATCAT
* * *
55176 GCGAAACTA-AGCAGGGGCCCCGAAACGCGTTTTTAGTTAAAAACCGTGATAGTTAATACACAAT
195 GCAAAAC-AGAGCAGGGG-CCCGAAACGCGTTTTTAG-CAAAAA-CGTGATGGTTAATACACAAT
* * * ** *
55240 TTCGGCTAAAATATTGCAGAAAAAAATCCGAAAATTTTGTCCTCAATTTTTTGAGACAATACTCG
256 TTCGGCTAAAATATTGCAGAAACAAATCCGAAAATTTTTTCCTCCATTTTTTGCCACAATACTCA
* * *
55305 GAAAAACATATATAATTCAACACCAAAAAAATGAAGGGTTTTTGATGCTTCTAATATTATTTTTC
321 GAAAAACATATATAATTCAACACCAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTTC
* * * * *
55370 C---TTTT-TTTTCGAATTTATCACTAATTAAATCGAAACAAGATACAAGTGCTCGTAAATACAA
386 CATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAA
*
55431 ATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATAAATATAGATATTTCAAGGTGTCTTTCTG
451 ATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTTTCTG
* ** *
55496 CCAAAAAATCATGCAAAACTAAGTAAGGACCAAAACTCGTTTTTGGCTAAAAACCGTGATGGTTA
516 CCGAAAAATCATGCAAAACTAAGTGGGGCCCAAAACTCGTTTTTGGCTAAAAACCGTGATGGTTA
55561 GTACACAAT
581 GTACACAAT
Statistics
Matches: 1144, Mismatches: 97, Indels: 38
0.89 0.08 0.03
Matches are distributed among these distances:
661 43 0.04
662 134 0.12
663 4 0.00
665 3 0.00
666 353 0.31
667 190 0.17
668 254 0.22
669 1 0.00
670 108 0.09
671 52 0.05
672 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (661 bp):
ATATATAATTCAACGCCAAAAAAATTGAAGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
TTCGAATTTATCTCTAATTAAATCGAAACAAGATTCATGGGCTTGTAAAAACAAATCCTTAAATC
CATTGTGGCTTAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGCAAAAATCATG
CAAAACAGAGCAGGGGCCCGAAACGCGTTTTTAGCAAAAACGTGATGGTTAATACACAATTTCGG
CTAAAATATTGCAGAAACAAATCCGAAAATTTTTTCCTCCATTTTTTGCCACAATACTCAGAAAA
ACATATATAATTCAACACCAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTTCCATTT
TTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATCCT
TAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTTTCTGCCGAA
AAATCATGCAAAACTAAGTGGGGCCCAAAACTCGTTTTTGGCTAAAAACCGTGATGGTTAGTACA
CAATTTCAGCTAAAATATTGCAAAAACTGAACCGAAAATTTTTTCATCAACTTTTTGCCACAATA
AACAGAAAAAA
Found at i:55405 original size:330 final size:333
Alignment explanation
Indices: 53636--55569 Score: 2513
Period size: 330 Copynumber: 5.8 Consensus size: 333
53626 CGTGTTTAGC
*
53636 GAAAAACCATATATAATTCAACACCAAAAAAATTGAAGAGTTTTTCATGCTTCTAATATCATTTT
1 GAAAAA-CATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTT
* * * *
53701 TCAATTTTTTTTCGAATTTATCTCCAATTAAATCGAAACAAGATTCAGGTGCTCGTAAATACAGA
65 TC-CTTTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAA
* * *
53766 TCCATAAATCCATTTTGACTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
129 TCCTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCTGC
* * * *
53831 TAAAAAATCATGCAAAACTGAGTC-GGGGCACCAAAACGCGTTTTTGGCTAAAAATCATGATGGT
194 CAAAAAATCATGCAAAACTAAGTCAGGGGC-CCAAAACGCGTTTTTGGCTAAAAACCGTGATGGT
* *
53895 TAGTACACAATTTCGGCTAAAATGTTGCAAAAACAAACCCGAAAATTTTTTCCTCCATTTTTTGC
258 TAGTACACAATTTCGGCTAAAATATTGCAAAAACAAACCCGAAAATTTTTTCCTCAATTTTTTGC
53960 CACAATACTCA
323 CACAATACTCA
53971 GAAAAACATATATAATTCAACACC-AAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
1 GAAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
*
54035 CCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACA
66 CC---TTTT-TTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACA
* * *
54100 AATCCTTAAATCCATTGTGAATGAAATTTGGTTAGATGAATATAGATATTTCAAGGTGTCTTTCT
127 AATCCTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCT
* * ** *
54165 GCCGAAAAATCATGCAAAACTAAGTAAGGACCCCCAAAACTCGTTTTTGGCTAAAAACCGTGATG
192 GCCAAAAAATCATGCAAAACTAAGTCAGG-GGCCCAAAACGCGTTTTTGGCTAAAAACCGTGATG
* * *** * *
54230 GTTAGTACACAATTTCAGCTAAAATATTGTAAAAATTGACCCGAAAATTTTTTCATCAACTTTTT
256 GTTAGTACACAATTTCGGCTAAAATATTGCAAAAACAAACCCGAAAATTTTTTCCTCAATTTTTT
** **
54295 GTTACAATAAACA
321 GCCACAATACTCA
* * * * ** * * *
54308 GAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTTTTAACACTTCTAAAATCGTTTTC
1 GAAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
* * *
54373 CCATTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCATGG-ACTTGTAAAAACAAAT
66 CCTTTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCA-GGTGCTCGTAAAAACAAAT
* * * * * *
54437 CCTTAAATCCAATGTGGCTTAGATTTGGTTAGATGAAAATAGATATTTCAAGGAGACTTTTTGCC
130 CCTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCTGCC
* * * * * *
54502 --AAAATCATGCAAAAC-AGAG-CAGGGGCCCGAAACACGGTTTTAGC-CAAAACGGTGATGGTT
195 AAAAAATCATGCAAAACTA-AGTCAGGGGCCCAAAACGCGTTTTTGGCTAAAAACCGTGATGGTT
* * * * *
54562 AATACACAATTTCGGCTAAAATATTGCAGAAACAAATTCCGAAATTTTTTTCCTCCATTTTTTGC
259 AGTACACAATTTCGGCTAAAATATTGCAAAAACAAA-CCCGAAAATTTTTTCCTCAATTTTTTGC
54627 CACAATACTCA
323 CACAATACTCA
* *
54638 GAAAAACATATATAATTCAACACCAAAAATATTGAAAGGTTTTTCATGCTTCTAATATCATTTTT
1 GAAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
*
54703 CCATTTTTTGTTTTCGAATTTATCTCTAAATAAATCGAAACAAGATTCAGGTGCTCGTAAAAACA
66 CC---TTTT-TTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACA
** * *
54768 AATCCTTAAATCCATTGTGGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCT
127 AATCCTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCT
* * * * *
54833 GCCGAAAAATCATGCAAAACTGAGTC-GGGGCCCGAAATGCGTTTTTGGCTAAAAACTGTGATGG
192 GCCAAAAAATCATGCAAAACTAAGTCAGGGGCCCAAAACGCGTTTTTGGCTAAAAACCGTGATGG
*
54897 TTAGTACACAATTTCGGCTAAAATATTGCAAAAACTGAA-CCGAAAATTTTTTTCCTCAATTTTT
257 TTAGTACACAATTTCGGCTAAAATATTGCAAAAAC-AAACCCGAAAA-TTTTTTCCTCAATTTTT
**
54961 TGCCACAATAAACA
320 TGCCACAATACTCA
* ** * *
54975 GAAAAA-ATATATAATTCAACGCCAAAAAAATTGAAGTATTTTTCACGCTTCTAATATCGTTTTT
1 GAAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
* * *
55039 CCATTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAAATTCATGG-GCTTGTAAAAACAAAT
66 CCTTTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCA-GGTGCTCGTAAAAACAAAT
* * * * * *
55103 CCTTAAATCCATTGTGGCTTAGATTTGATTAGATGAAAATAGATATTTCAAGGAGACTTTTTG-C
130 CCTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCTGCC
* * * * *
55167 -AAAAATCATGCGAAACTAAG-CAGGGGCCCCGAAACGCGTTTTTAGTTAAAAACCGTGATAGTT
195 AAAAAATCATGCAAAACTAAGTCAGGGG-CCCAAAACGCGTTTTTGGCTAAAAACCGTGATGGTT
* * * *
55230 AATACACAATTTCGGCTAAAATATTGCAGAAAA-AAATCCGAAAATTTTGTCCTCAATTTTTTGA
259 AGTACACAATTTCGGCTAAAATATTGCA-AAAACAAACCCGAAAATTTTTTCCTCAATTTTTTGC
* *
55294 GACAATACTCG
323 CACAATACTCA
* *
55305 GAAAAACATATATAATTCAACACCAAAAAAA-TGAAGGGTTTTTGATGCTTCTAATATTATTTTT
1 GAAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
* * * *
55369 CCTTTTTTTTCGAATTTATCACTAATTAAATCGAAACAAGATACAAGTGCTCGTAAATACAAATC
66 CCTTTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATC
* *
55434 CTTAAATCCATTGTGAATGAAATTTGGTTAGAT-AAATATAGATATTTCAAGGTGTCTTTCTGCC
131 CTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAA-ATAGATATTTCAAGGAGTCTTTCTGCC
* * *
55498 AAAAAATCATGCAAAACTAAGT-A-AGGACCAAAACTCGTTTTTGGCTAAAAACCGTGATGGTTA
195 AAAAAATCATGCAAAACTAAGTCAGGGGCCCAAAACGCGTTTTTGGCTAAAAACCGTGATGGTTA
55561 GTACACAAT
260 GTACACAAT
Statistics
Matches: 1389, Mismatches: 177, Indels: 71
0.85 0.11 0.04
Matches are distributed among these distances:
329 48 0.03
330 328 0.24
331 96 0.07
332 150 0.11
333 50 0.04
334 237 0.17
335 15 0.01
336 229 0.16
337 198 0.14
338 38 0.03
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (333 bp):
GAAAAACATATATAATTCAACACCAAAAAAATTGAAGGGTTTTTCATGCTTCTAATATCATTTTT
CCTTTTTTTTCGAATTTATCTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAAAACAAATC
CTTAAATCCATTGTGACTGAAATTTGGTTAGATGAAAATAGATATTTCAAGGAGTCTTTCTGCCA
AAAAATCATGCAAAACTAAGTCAGGGGCCCAAAACGCGTTTTTGGCTAAAAACCGTGATGGTTAG
TACACAATTTCGGCTAAAATATTGCAAAAACAAACCCGAAAATTTTTTCCTCAATTTTTTGCCAC
AATACTCA
Done.