Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013236.1 Kokia drynarioides strain JFW-HI SEQ_128255, 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: 477469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:329693 original size:88 final size:87
Alignment explanation
Indices: 329548--329714 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 87
329538 ACCCCAAACT
* * *
329548 TCCCTAAACTTCTTAAAAATTACCTTTTATACCTAAACTTTCCAAAAATTACATTTTAACCCATA
1 TCCCTAAACTTCTTAAAAATTACATTTTATACCCAAACTTTCCAAAAATCACATTTT-ACCC-TA
329613 AA-ATTCTCTAAAATTACATTTTGA
64 AACATT-TCTAAAATTACATTTTGA
*
329637 TCCCT-AACTTCTTCAAAATTACATTTTA-ACCCCAAACTTT-C-AAAATCACATTTTTTACCCT
1 TCCCTAAACTTCTTAAAAATTACATTTTATA-CCCAAACTTTCCAAAAATCACA--TTTTACCCT
*
329698 AAACCTTTCTAAAATTA
63 AAACATTTCTAAAATTA
329715 AAGTTCTACC
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
86 22 0.32
87 8 0.12
88 34 0.49
89 5 0.07
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.38
Consensus pattern (87 bp):
TCCCTAAACTTCTTAAAAATTACATTTTATACCCAAACTTTCCAAAAATCACATTTTACCCTAAA
CATTTCTAAAATTACATTTTGA
Found at i:329814 original size:29 final size:28
Alignment explanation
Indices: 329725--329827 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 28
329715 AAGTTCTACC
* *
329725 CCAAAGATTACCATTTTGA-CATCGAACAT
1 CCAAAAATTACCATTTT-ACCCTCGAA-AT
* *
329754 CTAAAAAATACCATTTTTACCCTCGAAAT
1 CCAAAAATTACCA-TTTTACCCTCGAAAT
*
329783 CCAAAAATTACCATTTTGCCCTC-AAATTT
1 CCAAAAATTACCATTTTACCCTCGAAA--T
*
329812 CCAAAAATCA-CATTTT
1 CCAAAAATTACCATTTT
329828 CAACTTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
27 3 0.05
28 15 0.24
29 34 0.55
30 10 0.16
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (28 bp):
CCAAAAATTACCATTTTACCCTCGAAAT
Found at i:331600 original size:14 final size:15
Alignment explanation
Indices: 331577--331627 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
331567 GTGACAAAAT
*
331577 AAAATGGAAATGCTA
1 AAAATAGAAATGCTA
331592 AAAAT-GAAAT-CTA
1 AAAATAGAAATGCTA
*
331605 CAAAATCATAAATGCTA
1 -AAAAT-AGAAATGCTA
331622 AAAATA
1 AAAATA
331628 AAAAAGGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 3 0.10
14 10 0.32
15 6 0.19
16 9 0.29
17 3 0.10
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (15 bp):
AAAATAGAAATGCTA
Found at i:331922 original size:13 final size:12
Alignment explanation
Indices: 331882--331931 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
331872 TGAAATAGAG
331882 TGAAAATAATAAA
1 TGAAAATAA-AAA
*
331895 TGGAAAATCAAAA
1 T-GAAAATAAAAA
331908 TGAAAATAAAGAA
1 TGAAAATAAA-AA
*
331921 TGGAAATAAAA
1 TGAAAATAAAA
331932 TAAAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 9 0.28
13 16 0.50
14 7 0.22
ACGTcount: A:0.66, C:0.02, G:0.14, T:0.18
Consensus pattern (12 bp):
TGAAAATAAAAA
Found at i:331922 original size:26 final size:24
Alignment explanation
Indices: 331859--331937 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
331849 ATTTTCTCAT
* *
331859 AAAATAATATATAT-GAAATAGAGTG
1 AAAATAATA-A-ATGGAAATAAAATG
331884 AAAATAATAAATGGAAAATCAAAATG
1 AAAATAATAAATGG-AAAT-AAAATG
331910 AAAATAA-AGAATGGAAATAAAAT-
1 AAAATAATA-AATGGAAATAAAATG
331933 AAAAT
1 AAAAT
331938 TTTAAAGGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.15
24 7 0.15
25 18 0.38
26 16 0.33
ACGTcount: A:0.65, C:0.01, G:0.13, T:0.22
Consensus pattern (24 bp):
AAAATAATAAATGGAAATAAAATG
Found at i:336510 original size:23 final size:24
Alignment explanation
Indices: 336484--336530 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
336474 ACTGCTGTTG
*
336484 TCCA-AATTGTTTGCACTATCTTT
1 TCCATAATTCTTTGCACTATCTTT
*
336507 TCCATATTTCTTTGCACTATCTTT
1 TCCATAATTCTTTGCACTATCTTT
336531 CATTCAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.51
Consensus pattern (24 bp):
TCCATAATTCTTTGCACTATCTTT
Found at i:336861 original size:26 final size:26
Alignment explanation
Indices: 336814--336869 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
336804 ATTTCTTCCA
*
336814 TTCTTCTTCATTTCCATGCCTTTCTC
1 TTCTTCATCATTTCCATGCCTTTCTC
* *
336840 TTCTTCATCACTTTCC-TTCCTTTTTC
1 TTCTTCATCA-TTTCCATGCCTTTCTC
336866 TTCT
1 TTCT
336870 CATTTTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.07, C:0.34, G:0.02, T:0.57
Consensus pattern (26 bp):
TTCTTCATCATTTCCATGCCTTTCTC
Found at i:337211 original size:9 final size:9
Alignment explanation
Indices: 337197--337224 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
337187 ATATCTCCAA
337197 AATATCATC
1 AATATCATC
337206 AATATCATC
1 AATATCATC
337215 AATATCATC
1 AATATCATC
337224 A
1 A
337225 TTATATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (9 bp):
AATATCATC
Found at i:367140 original size:20 final size:20
Alignment explanation
Indices: 367115--367152 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
367105 GCTTAAAATA
*
367115 TTTTTTTTATGTTTCTTTTT
1 TTTTTTTTATATTTCTTTTT
*
367135 TTTTTTTTTTATTTCTTT
1 TTTTTTTTATATTTCTTT
367153 CATTTATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.05, G:0.03, T:0.87
Consensus pattern (20 bp):
TTTTTTTTATATTTCTTTTT
Found at i:369554 original size:5 final size:5
Alignment explanation
Indices: 369544--369568 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
369534 AATTTCATCC
369544 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
369569 CATTTACCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:370830 original size:116 final size:116
Alignment explanation
Indices: 370626--370857 Score: 437
Period size: 116 Copynumber: 2.0 Consensus size: 116
370616 GTATACACAG
370626 ATATACATTATATAAGCAAAAAAACACATCTCTATATAGACTAGCTCAAGTCATTCCTATCTGCA
1 ATATACATTATATAAGCAAAAAAACACATCTCTATATAGACTAGCTCAAGTCATTCCTATCTGCA
370691 ACAGTGGTACCCAAGGTACTGACTTTCTATCTGAATTCCTCTGGGTCAGGT
66 ACAGTGGTACCCAAGGTACTGACTTTCTATCTGAATTCCTCTGGGTCAGGT
* *
370742 ATATACATTATATGAGCAAAAAAGCACATCTCTATATAGACTAGCTCAAGTCATTCCTATCTGCA
1 ATATACATTATATAAGCAAAAAAACACATCTCTATATAGACTAGCTCAAGTCATTCCTATCTGCA
*
370807 ACAGTGGTACCCAAGGTACTGACTTTCTCTCTGAATTCCTCTGGGTCAGGT
66 ACAGTGGTACCCAAGGTACTGACTTTCTATCTGAATTCCTCTGGGTCAGGT
370858 CAGTTTCCTT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (116 bp):
ATATACATTATATAAGCAAAAAAACACATCTCTATATAGACTAGCTCAAGTCATTCCTATCTGCA
ACAGTGGTACCCAAGGTACTGACTTTCTATCTGAATTCCTCTGGGTCAGGT
Found at i:373327 original size:5 final size:5
Alignment explanation
Indices: 373317--373342 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
373307 CTTGTATACC
373317 CACCA CACCA CACCA CACCA CACCA C
1 CACCA CACCA CACCA CACCA CACCA C
373343 TGCACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCA
Found at i:380202 original size:15 final size:15
Alignment explanation
Indices: 380167--380205 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
380157 TTAATATTAC
* *
380167 ATTTTTTACTTTTTT
1 ATTTTTTAATTTTTA
*
380182 ACTTTTTAATTTTTA
1 ATTTTTTAATTTTTA
380197 ATTTTTTAA
1 ATTTTTTAA
380206 ATTAAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTTTAATTTTTA
Found at i:380468 original size:16 final size:17
Alignment explanation
Indices: 380410--380468 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
380400 TAGAGCATAT
380410 ATAAATATAAAATTATAA
1 ATAAAT-TAAAATTATAA
* *
380428 AAAAATTAAATATTATCA
1 ATAAATTAAA-ATTATAA
*
380446 AT--TTTAAAATTA-AA
1 ATAAATTAAAATTATAA
380460 ATAAATTAA
1 ATAAATTAA
380469 TTTATATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 9 0.28
17 4 0.12
18 12 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAAATTAAAATTATAA
Found at i:380478 original size:2 final size:2
Alignment explanation
Indices: 380471--380507 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
380461 TAAATTAATT
*
380471 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
380508 TAAAAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:385409 original size:2 final size:2
Alignment explanation
Indices: 385404--385444 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
385394 TGTTTTTTAA
385404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
385445 AATTTTGCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:399361 original size:17 final size:17
Alignment explanation
Indices: 399339--399375 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
399329 TTTTCATATA
399339 AAAAAGGAAAAAG-AAAT
1 AAAAA-GAAAAAGAAAAT
399356 AAAAAGAAAAAGAAAAT
1 AAAAAGAAAAAGAAAAT
399373 AAA
1 AAA
399376 GAAAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAT
Found at i:399364 original size:16 final size:15
Alignment explanation
Indices: 399338--399379 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
399328 ATTTTCATAT
*
399338 AAAAAAGGAAAAAGA
1 AAAAAAAGAAAAAGA
399353 AATAAAAAGAAAAAGA
1 AA-AAAAAGAAAAAGA
*
399369 AAATAAAGAAA
1 AAAAAAAGAAA
399380 GTAAAAGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAAAAGAAAAAGA
Found at i:399474 original size:6 final size:6
Alignment explanation
Indices: 399463--399487 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
399453 AATGGGAAAG
399463 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
399488 CTAATAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:399532 original size:18 final size:18
Alignment explanation
Indices: 399498--399550 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
399488 CTAATAAGTG
* *
399498 ATTTTTTAATCATTTAAT
1 ATTTTTTAATAAATTAAT
399516 ATTTTTTAATAAATTAAT
1 ATTTTTTAATAAATTAAT
* * *
399534 CTATTTTAAAAAATTAA
1 ATTTTTTAATAAATTAA
399551 AAAATGTCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTTAATAAATTAAT
Found at i:402511 original size:21 final size:21
Alignment explanation
Indices: 402493--402534 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
402483 TTCTTTTTGT
402493 TGTTTT-CTTGCTATTTTTTAC
1 TGTTTTGCTT-CTATTTTTTAC
402514 TGTTTTGCTTCTATTGTTTTA
1 TGTTTTGCTTCTATT-TTTTA
402535 TCAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.67
Consensus pattern (21 bp):
TGTTTTGCTTCTATTTTTTAC
Found at i:402801 original size:11 final size:11
Alignment explanation
Indices: 402785--402810 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
402775 TAATATTTTT
402785 ATTTAGATAAA
1 ATTTAGATAAA
402796 ATTTAGATAAA
1 ATTTAGATAAA
402807 ATTT
1 ATTT
402811 TAAACCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (11 bp):
ATTTAGATAAA
Found at i:404649 original size:24 final size:23
Alignment explanation
Indices: 404622--404709 Score: 55
Period size: 24 Copynumber: 3.9 Consensus size: 23
404612 TTAGGGTTTA
404622 AGAACCTGGAGGCAATAAGACCAT
1 AGAACCTGGAGG-AATAAGACCAT
*
404646 AGAACTTGGACGGAATGACAGA-CATT
1 AGAACCTGGA-GGAAT-A-AGACCA-T
404672 A-AA-C--G-GG-ATAAGACCAT
1 AGAACCTGGAGGAATAAGACCAT
*
404689 AGAACTTGGAGGCAATAAGAC
1 AGAACCTGGAGG-AATAAGAC
404710 TCTGGAAGAT
Statistics
Matches: 49, Mismatches: 3, Indels: 24
0.64 0.04 0.32
Matches are distributed among these distances:
17 5 0.10
18 5 0.10
19 2 0.04
20 2 0.04
21 1 0.02
22 3 0.06
24 19 0.39
25 7 0.14
26 5 0.10
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (23 bp):
AGAACCTGGAGGAATAAGACCAT
Found at i:407238 original size:78 final size:78
Alignment explanation
Indices: 407104--407249 Score: 179
Period size: 78 Copynumber: 1.9 Consensus size: 78
407094 TTACAATAGT
* * * *
407104 TAAAACATAATTTTATTAGTTTATTAGTTTATATTTTTATAATTTAAAAAAATTAAAT-TAAATT
1 TAAAACATAATTTTATTAG-TTATTAATTTAAAATTTTATAATTTAAAAAAATTAAATGAAAATT
407168 TTTATCATTTGGGA
65 TTTATCATTTGGGA
* ** *
407182 TAAAATATAATTTTATTA-TTATTAATTTAAAATTTTATAAATTATAAAGGATTTAAATGAAAAT
1 TAAAACATAATTTTATTAGTTATTAATTTAAAATTTTAT-AATT-TAAAAAAATTAAATGAAAAT
407246 TTTT
64 TTTT
407250 TTATTTTAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
76 17 0.30
77 4 0.07
78 28 0.49
79 8 0.14
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (78 bp):
TAAAACATAATTTTATTAGTTATTAATTTAAAATTTTATAATTTAAAAAAATTAAATGAAAATTT
TTATCATTTGGGA
Found at i:407574 original size:39 final size:40
Alignment explanation
Indices: 407514--407590 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
407504 AAGAGGTATG
*
407514 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* *
407554 TCCAATTTG-AAAGGATTGTGACTCTTCAAAATGTGTC
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTC
407591 AATTAAGTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 26 0.76
40 8 0.24
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:415524 original size:27 final size:28
Alignment explanation
Indices: 415498--415564 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 28
415488 GAAGGCCAAA
415498 AATATAAATAGCATAAA-AAATAACAAAAT
1 AATA-AAATA-CATAAATAAATAACAAAAT
*
415527 AATAAAATACATAAATAAATGAATAAAATT
1 AATAAAATACATAAATAAAT-AACAAAA-T
415557 AAATAAAA
1 -AATAAAA
415565 CAAGCATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.18
28 9 0.27
29 10 0.30
30 1 0.03
31 7 0.21
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.22
Consensus pattern (28 bp):
AATAAAATACATAAATAAATAACAAAAT
Found at i:415719 original size:4 final size:4
Alignment explanation
Indices: 415710--415734 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
415700 AAATTTAATG
415710 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
415735 CACGATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:415826 original size:14 final size:15
Alignment explanation
Indices: 415807--415842 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
415797 TCAAGATAAT
415807 AAATAAC-CACAAAA
1 AAATAACACACAAAA
415821 AAATAAACACACAAAA
1 AAAT-AACACACAAAA
415837 AAATAA
1 AAATAA
415843 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 5 0.25
16 11 0.55
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (15 bp):
AAATAACACACAAAA
Found at i:417442 original size:50 final size:51
Alignment explanation
Indices: 417347--417544 Score: 141
Period size: 50 Copynumber: 3.9 Consensus size: 51
417337 CTTTAAGAAG
* * * * * *
417347 ATAGAATTTGCTTTCTTTAACTTCAATCTGCCCCTCTATAGCTTTAGGGGA
1 ATAGGATTTGCTTTCTGTAAATTCAATCTACCCCTCTACAACTTTAGGGGA
* *
417398 ATAGGATTTGCTTT-TGTAAATTTAATCTACCCCTCTACAACTTTAGGGGT
1 ATAGGATTTGCTTTCTGTAAATTCAATCTACCCCTCTACAACTTTAGGGGA
* * * *** * * * * *
417448 ATAAGATTCGCGTTC-GTGGCTTCAATCTGCCCTTTTACAACTTTAGAGGC
1 ATAGGATTTGCTTTCTGTAAATTCAATCTACCCCTCTACAACTTTAGGGGA
* ** ** * *
417498 ATAAGATTCACTTT-TGTAGCTTCAATCTACCCCTCTATAGCTTTAGG
1 ATAGGATTTGCTTTCTGTAAATTCAATCTACCCCTCTACAACTTTAGG
417545 AGTATAAGAT
Statistics
Matches: 116, Mismatches: 29, Indels: 5
0.77 0.19 0.03
Matches are distributed among these distances:
50 103 0.89
51 13 0.11
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (51 bp):
ATAGGATTTGCTTTCTGTAAATTCAATCTACCCCTCTACAACTTTAGGGGA
Found at i:417512 original size:100 final size:100
Alignment explanation
Indices: 417367--418003 Score: 639
Period size: 100 Copynumber: 6.4 Consensus size: 100
417357 CTTTCTTTAA
* * ** * ** *
417367 CTTCAATCTGCCCCTCTATAGCTTTAGGGGAATAGGATTTGCTTTTGTAAATTTAATCTACCCCT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
* * * *
417432 CTACAACTTTAGGGGTATAAGATTCGCGTTCGTGG
66 CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
* * * * * * *
417467 CTTCAATCTGCCCTTTTACAACTTTAGAGGCATAAGATTCACTTTTGTAGCTTCAATCTACCCCT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
* *
417532 CTATAGCTTTAGGAGTATAAGATTCACCTTCGCGG
66 CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
* * * **
417567 CTTCACTCTGCCCCTTTATAACTTTA-GGGTATAAGATTCACCTTTGCGGCTTCAATCTACCCCT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
* * * * * **
417631 CTACAGCTTGAGGTGTGTAAGATTCACTTTTGTAG
66 CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
* * ** * *
417666 CTTCAATATGCCCCTCTACAGCTTTAGGGGTATAAGATTTGCCTTCGTAGCTTCAATCTGCCCCT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
*
417731 CTATAGCTTTAGGGGTATAAGATTCACCTTCGCGG
66 CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
* * * * * *
417766 CTTGAATCTGCCCCTCTATTGCTTTAGAGGTATAAGATTCACTTTTGCAGCTTCAATCTATCCCT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
* * * * **
417831 CTACAACTTTAAGGGTATAAGATTCGCTTTTACGG
66 CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
* * * * ** * * * *
417866 CTTAAATATGCCCTTTTATAGCTTTAGGGGTATAAGATTCACCTTCATAGTTTTAATTTGCCCCT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
* *
417931 CTACAGCTTTAGAGGTATAAGATTCACCTTCACGG
66 CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
* ** * *
417966 CTTCAATTTATCCCTTTATTGCTTTA-GGGTATAAGATT
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATT
418004 TGCCTTCGCG
Statistics
Matches: 437, Mismatches: 99, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
99 93 0.21
100 344 0.79
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (100 bp):
CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTTGTAGCTTCAATCTACCCCT
CTACAGCTTTAGGGGTATAAGATTCACCTTCGCGG
Found at i:417552 original size:50 final size:50
Alignment explanation
Indices: 417367--418037 Score: 556
Period size: 50 Copynumber: 13.5 Consensus size: 50
417357 CTTTCTTTAA
* * ** * * * *
417367 CTTCAATCTGCCCCTCTATAGCTTTAGGGGAATAGGATTTGCTTTTGTAA
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * * * * **
417417 ATTTAATCTACCCCTCTACAACTTTAGGGGTATAAGATTCGCGTTCGTGG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * * * * * *
417467 CTTCAATCTGCCCTTTTACAACTTTAGAGGCATAAGATTCACTTTTGTAG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * *
417517 CTTCAATCTACCCCTCTATAGCTTTAGGAGTATAAGATTCACCTTCGCGG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * *
417567 CTTCACTCTGCCCCTTTATAACTTTA-GGGTATAAGATTCACCTTTGCGG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * * * * *
417616 CTTCAATCTACCCCTCTACAGCTTGAGGTGTGTAAGATTCACTTTTGTAG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * ** *
417666 CTTCAATATGCCCCTCTACAGCTTTAGGGGTATAAGATTTGCCTTCGTAG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
*
417716 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCGG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * *
417766 CTTGAATCTGCCCCTCTATTGCTTTAGAGGTATAAGATTCACTTTTGCAG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
** * * * * * ** *
417816 CTTCAATCTATCCCTCTACAACTTTAAGGGTATAAGATTCGCTTTTACGG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * **
417866 CTTAAATATGCCCTTTTATAGCTTTAGGGGTATAAGATTCACCTTCATAG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* * * * * * *
417916 TTTTAATTTGCCCCTCTACAGCTTTAGAGGTATAAGATTCACCTTCACGG
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
* ** * * **
417966 CTTCAATTTATCCCTTTATTGCTTTA-GGGTATAAGATTTGCCTTCGC-G
1 CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
*
418014 ACTTCAATCTGCCCCTTTATAGCT
1 -CTTCAATCTGCCCCTCTATAGCT
418038 ATAAGATTTG
Statistics
Matches: 497, Mismatches: 122, Indels: 5
0.80 0.20 0.01
Matches are distributed among these distances:
48 1 0.00
49 77 0.15
50 419 0.84
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTATAGCTTTAGGGGTATAAGATTCACCTTCGCAG
Found at i:417821 original size:150 final size:150
Alignment explanation
Indices: 417367--418037 Score: 697
Period size: 150 Copynumber: 4.5 Consensus size: 150
417357 CTTTCTTTAA
* * * * * ** * *
417367 CTTCAATCTGCCCCTCTATAGCTTTAGGGGAATAGGATTTGCTTTTGTAAATTTAATCTACCCCT
1 CTTCAATCTACCCCTCTATAGCTTTAGGGGTATAAGATTTGCCTTCGTAGCTTCAATCTGCCCCT
* * * * * * * * *
417432 CTACAACTTTAGGGGTATAAGATTCGCGTTCGTGGCTTCAATCTGCCCTTTTACAACTTTAGAGG
66 TTATAGCTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCTGCCCCTCTACAGCTTTAGAGG
* *
417497 CATAAGATTCACTTTTGTAG
131 TATAAGATTCACTTTTGCAG
* ** ** *
417517 CTTCAATCTACCCCTCTATAGCTTTAGGAGTATAAGATTCACCTTCGCGGCTTCACTCTGCCCCT
1 CTTCAATCTACCCCTCTATAGCTTTAGGGGTATAAGATTTGCCTTCGTAGCTTCAATCTGCCCCT
* * * *
417582 TTATAACTTTA-GGGTATAAGATTCACCTTTGCGGCTTCAATCTACCCCTCTACAGCTTGAG-GT
66 TTATAGCTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCTGCCCCTCTACAGCTTTAGAG-
* *
417645 GTGTAAGATTCACTTTTGTAG
130 GTATAAGATTCACTTTTGCAG
* * *
417666 CTTCAATATGCCCCTCTACAGCTTTAGGGGTATAAGATTTGCCTTCGTAGCTTCAATCTGCCCCT
1 CTTCAATCTACCCCTCTATAGCTTTAGGGGTATAAGATTTGCCTTCGTAGCTTCAATCTGCCCCT
* * **
417731 CTATAGCTTTAGGGGTATAAGATTCACCTTCGCGGCTTGAATCTGCCCCTCTATTGCTTTAGAGG
66 TTATAGCTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCTGCCCCTCTACAGCTTTAGAGG
417796 TATAAGATTCACTTTTGCAG
131 TATAAGATTCACTTTTGCAG
* * * * * * * *
417816 CTTCAATCTATCCCTCTACAACTTTAAGGGTATAAGATTCG-CTT-TTACGGCTTAAATATGCCC
1 CTTCAATCTACCCCTCTATAGCTTTAGGGGTATAAGATTTGCCTTCGTA--GCTTCAATCTGCCC
* *** * * *
417879 TTTTATAGCTTTAGGGGTATAAGATTCACCTTCATAGTTTTAATTTGCCCCTCTACAGCTTTAGA
64 CTTTATAGCTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCTGCCCCTCTACAGCTTTAGA
* ** *
417944 GGTATAAGATTCACCTTCACGG
129 GGTATAAGATTCACTTTTGCAG
* * * * *
417966 CTTCAATTTATCCCTTTATTGCTTTA-GGGTATAAGATTTGCCTTCG-CGACTTCAATCTGCCCC
1 CTTCAATCTACCCCTCTATAGCTTTAGGGGTATAAGATTTGCCTTCGTAG-CTTCAATCTGCCCC
418029 TTTATAGCT
65 TTTATAGCT
418038 ATAAGATTTG
Statistics
Matches: 432, Mismatches: 81, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
148 4 0.01
149 161 0.37
150 266 0.62
151 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (150 bp):
CTTCAATCTACCCCTCTATAGCTTTAGGGGTATAAGATTTGCCTTCGTAGCTTCAATCTGCCCCT
TTATAGCTTTAGGGGTATAAGATTCACCTTCGCGGCTTCAATCTGCCCCTCTACAGCTTTAGAGG
TATAAGATTCACTTTTGCAG
Found at i:418435 original size:15 final size:15
Alignment explanation
Indices: 418410--418450 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
418400 AAAAGGTATG
*
418410 ATGCGAGCATGAGTA
1 ATGCGAGCATGAATA
* *
418425 GTGCGAACATGAATA
1 ATGCGAGCATGAATA
418440 ATGCGAGCATG
1 ATGCGAGCATG
418451 GACCTTGCGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.32, T:0.20
Consensus pattern (15 bp):
ATGCGAGCATGAATA
Found at i:418520 original size:30 final size:30
Alignment explanation
Indices: 418498--418568 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
418488 TGAGCACTTG
418498 TGTTGCGAACACTGGAGCTGTGAACACTCA
1 TGTTGCGAACACTGGAGCTGTGAACACTCA
* * *
418528 TGTTACGAACATTGGAGTTGTGAACACTCA
1 TGTTGCGAACACTGGAGCTGTGAACACTCA
418558 TGTTGCGAACA
1 TGTTGCGAACA
418569 AACACAATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (30 bp):
TGTTGCGAACACTGGAGCTGTGAACACTCA
Found at i:423352 original size:24 final size:24
Alignment explanation
Indices: 423283--423343 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
423273 CGTTATTCTG
* * * *
423283 ATTCTGGGCTTGCAAGACCTAATC
1 ATTCTGGGCTCGTAAGAGCTAACC
423307 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
423331 ATTTTGGGCTCGT
1 ATTCTGGGCTCGT
423344 GTGGGCTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:430470 original size:30 final size:30
Alignment explanation
Indices: 430430--430486 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
430420 CGAGCGCTCG
* *
430430 TGTTGTGAACACTAGAGCTGTGAACACTCA
1 TGTTGCGAACAATAGAGCTGTGAACACTCA
*
430460 TGTTGCGAACAATAGAGTTGTGAACAC
1 TGTTGCGAACAATAGAGCTGTGAACAC
430487 ACACAATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (30 bp):
TGTTGCGAACAATAGAGCTGTGAACACTCA
Found at i:430500 original size:30 final size:30
Alignment explanation
Indices: 430433--430500 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
430423 GCGCTCGTGT
* * ***
430433 TGTGAACACTAGAGCTGTGAACACTCATGT
1 TGTGAACAATAGAGCTGTGAACACACACAA
* *
430463 TGCGAACAATAGAGTTGTGAACACACACAA
1 TGTGAACAATAGAGCTGTGAACACACACAA
430493 TGTGAACA
1 TGTGAACA
430501 CTGATGCTGC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (30 bp):
TGTGAACAATAGAGCTGTGAACACACACAA
Found at i:432695 original size:109 final size:109
Alignment explanation
Indices: 432499--432711 Score: 306
Period size: 109 Copynumber: 2.0 Consensus size: 109
432489 AAAATCAAGG
* * *
432499 CAATGTTATTTTATTTTAGGAACTCGAGAAATTGTGCCTTAACGTGCTGGGTACGATTTTTCTTT
1 CAATGTTATTTTATTTTAGGAAATCGAGAAATTGTGCCTTAACGTACTAGGTACGATTTTTCTTT
*
432564 GAACCTAAATAATTAAGTATCCTA-TTTAAAATCGATAAATACT
66 GAACCTAAATAATTAAGCATCCTATTTTAAAATCGATAAATACT
* * *
432607 CAATGTTTTTTTATTTTAGGGAAATCGAGAAATTGTGTCC-TAACGTATTAGGTATGATTTTTCT
1 CAATGTTATTTTATTTTA-GGAAATCGAGAAATTGTG-CCTTAACGTACTAGGTACGATTTTTCT
*
432671 TTGAACCTAAGTAATTGAA-CATCCTATTTTAAAATCGATAA
64 TTGAACCTAAATAATT-AAGCATCCTATTTTAAAATCGATAA
432712 GTGTTCTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
108 17 0.18
109 58 0.62
110 18 0.19
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (109 bp):
CAATGTTATTTTATTTTAGGAAATCGAGAAATTGTGCCTTAACGTACTAGGTACGATTTTTCTTT
GAACCTAAATAATTAAGCATCCTATTTTAAAATCGATAAATACT
Found at i:434472 original size:11 final size:11
Alignment explanation
Indices: 434456--434498 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
434446 TAATTACTAA
*
434456 AGAAAATGAAT
1 AGAAAATAAAT
434467 AGAAAATAAAT
1 AGAAAATAAAT
*
434478 AAAAAATAAAT
1 AGAAAATAAAT
434489 A-AAAA-AAAT
1 AGAAAATAAAT
434498 A
1 A
434499 AATATATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 5 0.17
10 4 0.13
11 21 0.70
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (11 bp):
AGAAAATAAAT
Found at i:443477 original size:22 final size:23
Alignment explanation
Indices: 443430--443480 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
443420 CTTTATTTGA
443430 TAAAATATTTTGATATAATAAAT
1 TAAAATATTTTGATATAATAAAT
*
443453 TAAAATATTTTTGA-AT-ATAAGT
1 TAAAATA-TTTTGATATAATAAAT
443475 TAAAAT
1 TAAAAT
443481 TGACAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 11 0.42
23 9 0.35
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
TAAAATATTTTGATATAATAAAT
Found at i:451729 original size:19 final size:19
Alignment explanation
Indices: 451691--451729 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
451681 TACAAAATCC
*
451691 AATTTAATTTTTCATTTTT
1 AATTTAATTTTTAATTTTT
451710 AATTT-ATTTTTAATTATTT
1 AATTTAATTTTTAATT-TTT
451729 A
1 A
451730 TTATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
AATTTAATTTTTAATTTTT
Found at i:452771 original size:60 final size:59
Alignment explanation
Indices: 452704--452834 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 59
452694 ACCCCAAAAA
* * *
452704 TTTCTAAAAATTTGAATTTAACCCTCGAATTTTTCAAAAATTCAAATTTGATCCC-TAAAC
1 TTTCTAAAAATTTGAATTTAACCCT-AAAATTTCCAAAAATTCAAATTTGA-CCCTTAAAC
* * *
452764 TTTCTAAAAATTTGAATTTGACCCTAAAATTTCCAAAAATTCTAATTTGACCCTTAAAG
1 TTTCTAAAAATTTGAATTTAACCCTAAAATTTCCAAAAATTCAAATTTGACCCTTAAAC
452823 TTT-TCAAAAATT
1 TTTCT-AAAAATT
452835 CAAATTACTT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 4 0.06
59 35 0.56
60 24 0.38
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (59 bp):
TTTCTAAAAATTTGAATTTAACCCTAAAATTTCCAAAAATTCAAATTTGACCCTTAAAC
Found at i:452788 original size:29 final size:28
Alignment explanation
Indices: 452701--452834 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 28
452691 TTAACCCCAA
*
452701 AAATTTCTAAAAATTTGAATTTAACCCT
1 AAATTTCTAAAAATTTGAATTTGACCCT
* * **
452729 CGAATTTTTCAAAAATTCAAATTTGATCCCT
1 -AAATTTCT-AAAAATTTGAATTTGA-CCCT
452760 AAACTTTCTAAAAATTTGAATTTGACCCT
1 AAA-TTTCTAAAAATTTGAATTTGACCCT
*
452789 AAAATTTCCAAAAATTCT-AATTTGACCCTT
1 -AAATTTCTAAAAATT-TGAATTTGACCC-T
452819 AAAGTTT-TCAAAAATT
1 AAA-TTTCT-AAAAATT
452835 CAAATTACTT
Statistics
Matches: 86, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
29 34 0.40
30 44 0.51
31 8 0.09
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.38
Consensus pattern (28 bp):
AAATTTCTAAAAATTTGAATTTGACCCT
Found at i:452835 original size:30 final size:28
Alignment explanation
Indices: 452734--452840 Score: 124
Period size: 30 Copynumber: 3.6 Consensus size: 28
452724 ACCCTCGAAT
452734 TTTTCAAAAATTCAAATTTGATCCCTAAA
1 TTTTCAAAAATTCAAATTTGA-CCCTAAA
* **
452763 CTTTCTAAAAATTTGAATTTGACCCTAAAA
1 TTTTC-AAAAATTCAAATTTGACCCT-AAA
* *
452793 TTTCCAAAAATTCTAATTTGACCCTTAAA
1 TTTTCAAAAATTCAAATTTGACCC-TAAA
452822 GTTTTCAAAAATTCAAATT
1 -TTTTCAAAAATTCAAATT
452841 ACTTGGTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 28 0.43
30 37 0.57
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (28 bp):
TTTTCAAAAATTCAAATTTGACCCTAAA
Found at i:452946 original size:16 final size:17
Alignment explanation
Indices: 452904--452949 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
452894 TATTTTTTAA
452904 ATTTTATT-T-TATTGT
1 ATTTTATTATGTATTGT
452919 ATTTTATGTATGTATTGT
1 ATTTTAT-TATGTATTGT
452937 -TTTTATTATGTAT
1 ATTTTATTATGTAT
452950 ACTTGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.25
16 8 0.29
17 7 0.25
18 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (17 bp):
ATTTTATTATGTATTGT
Found at i:454903 original size:31 final size:31
Alignment explanation
Indices: 454860--454931 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
454850 TGCATATTCA
*
454860 TTCACGCATTCATAAAATTTCGCATTGCATT
1 TTCATGCATTCATAAAATTTCGCATTGCATT
* *
454891 TTCATGCATTCATAAAGTTTTGCATTGCATT
1 TTCATGCATTCATAAAATTTCGCATTGCATT
454922 TTCATGCATT
1 TTCATGCATT
454932 AAAATTTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.43
Consensus pattern (31 bp):
TTCATGCATTCATAAAATTTCGCATTGCATT
Found at i:459762 original size:49 final size:48
Alignment explanation
Indices: 459709--459858 Score: 158
Period size: 49 Copynumber: 3.1 Consensus size: 48
459699 AACGACGAAC
* * *
459709 CTTGTACCTTAGGGACGTGATGGGAAAGATTGAAGCCACGACGGTGAAT
1 CTTGTACCCTAGGGATGTGA-GGGAAAGATTGAAGCCACAACGGTGAAT
* * * *
459758 CTTGTACCCTAGAGTTATG-GAGGGAAAGATTGAAGCTACAATGGTGAAC
1 CTTGTACCCTAG-G-GATGTGAGGGAAAGATTGAAGCCACAACGGTGAAT
* * * *
459807 CTTGTACCCTAGAGATGTGAAGGGAAAGATTGAGGCCGCAACGATGAAT
1 CTTGTACCCTAGGGATGTG-AGGGAAAGATTGAAGCCACAACGGTGAAT
459856 CTT
1 CTT
459859 ACACCTTGAA
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
47 3 0.04
48 1 0.01
49 73 0.89
50 3 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (48 bp):
CTTGTACCCTAGGGATGTGAGGGAAAGATTGAAGCCACAACGGTGAAT
Found at i:460235 original size:79 final size:77
Alignment explanation
Indices: 460138--460787 Score: 691
Period size: 79 Copynumber: 8.2 Consensus size: 77
460128 CAAGTTACAA
* * *
460138 CAATCCAATCTTTTACCCTAATCAGAGGCCAAATTGAAGACCATCTAATCTTTTACCCTGACCGT
1 CAATCCAATCTTTTACCCTAA-CAGAGG-CAAATTGAAGACCATCTGATCTCTTACCCTGACCAT
*
460203 GGGGTAGATTGAAG
64 GGGGCAGATTGAAG
* * * * * *
460217 CAATCCAATCTTTTACCCTAATTAAAGGCCAAATTGAAGACCAGCCGAACTCTTACCCTGACTAT
1 CAATCCAATCTTTTACCCTAA-CAGAGG-CAAATTGAAGACCATCTGATCTCTTACCCTGACCAT
460282 GGGGCAGATTGAAG
64 GGGGCAGATTGAAG
* * *
460296 CAATCCAATCTTCTACCCTAATCAGAGGGCAGATTAAAGACCAATC-GATCTCTTACCCTGACCA
1 CAATCCAATCTTTTACCCTAA-CAGA-GGCAAATTGAAGACC-ATCTGATCTCTTACCCTGACCA
* *
460360 TAGGGCAAATTGAAG
63 TGGGGCAGATTGAAG
* * * *
460375 CAATCCAATATTTTACCCTAACTAGAGGGTAGATTGAAGACCATCTGATCTCTTACCCCGACCAT
1 CAATCCAATCTTTTACCCTAAC-AGA-GGCAAATTGAAGACCATCTGATCTCTTACCCTGACCAT
460440 GGGGCAGATTGAAG
64 GGGGCAGATTGAAG
* * * *
460454 AAATCTAATCTTTTACCCTAACTAGAAGGCAGATTGAAGACCATCCGATCTCTTAGCCC-GACCA
1 CAATCCAATCTTTTACCCTAAC-AG-AGGCAAATTGAAGACCATCTGATCTCTTA-CCCTGACCA
460518 TGGGGCAGATTGAAG
63 TGGGGCAGATTGAAG
* * * ** * * *
460533 CAATTCAATTTTTTACCCTAACCAAAGGGCGGATTGAAGACCAT-TCGATCTTTTACCCCGACGA
1 CAATCCAATCTTTTACCCTAA-CAGA-GGCAAATTGAAGACCATCT-GATCTCTTACCCTGACCA
*
460597 TGGGGCATATTGAAG
63 TGGGGCAGATTGAAG
* * *
460612 CAATCCAATCTTTTACCCTAACTAGAGAGCAAATTAAAGACCATCCGATCTCTTATCCC-AACCA
1 CAATCCAATCTTTTACCCTAAC-AGAG-GCAAATTGAAGACCATCTGATCTCTTA-CCCTGACCA
460676 TGGGGCAGATTGAAG
63 TGGGGCAGATTGAAG
* * *
460691 TAATCCAAT-TTTTAACCCTAACCAGAAGGCAAATTGAAGACCATTTGATCTCTTA-CCTCGACT
1 CAATCCAATCTTTT-ACCCTAA-CAG-AGGCAAATTGAAGACCATCTGATCTCTTACCCT-GACC
* *
460754 ATGGGGCAAATTGAAA
62 ATGGGGCAGATTGAAG
*
460770 CAATACAATCTTTTACCC
1 CAATCCAATCTTTTACCC
460788 ATAAAGCTAT
Statistics
Matches: 488, Mismatches: 63, Indels: 40
0.83 0.11 0.07
Matches are distributed among these distances:
77 2 0.00
78 14 0.03
79 453 0.93
80 19 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (77 bp):
CAATCCAATCTTTTACCCTAACAGAGGCAAATTGAAGACCATCTGATCTCTTACCCTGACCATGG
GGCAGATTGAAG
Found at i:460428 original size:158 final size:157
Alignment explanation
Indices: 460138--460787 Score: 765
Period size: 158 Copynumber: 4.1 Consensus size: 157
460128 CAAGTTACAA
* * ** *
460138 CAATCCAATCTTTTACCCTAA-TCAGAGGCCAAATTGAAGACCATCTAATCTTTTA-CCCTGACC
1 CAATCCAATCTTTTACCCTAACT-AGAGGGCAAATTAAAGACCATCCGATCTCTTAGCCC-GACC
* * ** * * * *
460201 GTGGGGTAGATTGAAGCAATCCAATCTTTTACCCTAATTAAAGGCCAAATTGAAGACCAGCCGAA
64 ATGGGGCAGATTGAAGCAATCCAAT-TTTTACCCTAACCAAAGGGCAAATTGAAGACCATCTGAT
*
460266 CTCTTACCCTGACTATGGGGCAGATTGAAG
128 CTCTTACCCCGACTATGGGGCAGATTGAAG
* *
460296 CAATCCAATCTTCTACCCTAA-TCAGAGGGCAGATTAAAGACCAAT-CGATCTCTTA-CCCTGAC
1 CAATCCAATCTTTTACCCTAACT-AGAGGGCAAATTAAAGACC-ATCCGATCTCTTAGCCC-GAC
* * * * * *
460358 CATAGGGCAAATTGAAGCAATCCAATATTTTACCCTAACTAGAGGGTAGATTGAAGACCATCTGA
63 CATGGGGCAGATTGAAGCAATCCAAT-TTTTACCCTAACCAAAGGGCAAATTGAAGACCATCTGA
*
460423 TCTCTTACCCCGACCATGGGGCAGATTGAAG
127 TCTCTTACCCCGACTATGGGGCAGATTGAAG
* * * * *
460454 AAATCTAATCTTTTACCCTAACTAGAAGGCAGATTGAAGACCATCCGATCTCTTAGCCCGACCAT
1 CAATCCAATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCCGATCTCTTAGCCCGACCAT
* **
460519 GGGGCAGATTGAAGCAATTCAATTTTTTACCCTAACCAAAGGGCGGATTGAAGACCAT-TCGATC
66 GGGGCAGATTGAAGCAATCCAA-TTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCT-GATC
* * *
460583 TTTTACCCCGACGATGGGGCATATTGAAG
129 TCTTACCCCGACTATGGGGCAGATTGAAG
* * *
460612 CAATCCAATCTTTTACCCTAACTAGAGAGCAAATTAAAGACCATCCGATCTCTTATCCCAACCAT
1 CAATCCAATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCCGATCTCTTAGCCCGACCAT
* *
460677 GGGGCAGATTGAAGTAATCCAATTTTTAACCCTAACCAGAA-GGCAAATTGAAGACCATTTGATC
66 GGGGCAGATTGAAGCAATCCAATTTTT-ACCCTAACCA-AAGGGCAAATTGAAGACCATCTGATC
* * *
460741 TCTTACCTCGACTATGGGGCAAATTGAAA
129 TCTTACCCCGACTATGGGGCAGATTGAAG
*
460770 CAATACAATCTTTTACCC
1 CAATCCAATCTTTTACCC
460788 ATAAAGCTAT
Statistics
Matches: 428, Mismatches: 55, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
157 8 0.02
158 410 0.96
159 10 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (157 bp):
CAATCCAATCTTTTACCCTAACTAGAGGGCAAATTAAAGACCATCCGATCTCTTAGCCCGACCAT
GGGGCAGATTGAAGCAATCCAATTTTTACCCTAACCAAAGGGCAAATTGAAGACCATCTGATCTC
TTACCCCGACTATGGGGCAGATTGAAG
Found at i:460553 original size:237 final size:236
Alignment explanation
Indices: 460138--460787 Score: 856
Period size: 237 Copynumber: 2.7 Consensus size: 236
460128 CAAGTTACAA
* * * * *
460138 CAATCCAATCTTTTACCCTAA-TCAGAGGCCAAATTGAAGACCATCTAATCTTTTACCCTGACCG
1 CAATCCAATCTTTTACCCTAACT-AGAGGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCA
* * * * *
460202 TGGGGTAGATTGAAGCAATCCAATCTTTTACCCTAATTA-AAGGCCAAATTGAAGACCAGCCGAA
65 TGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAAGG-CAAATTGAAGACCATCCGAT
* * * *
460266 CTCTTACCCTGACTATGGGGCAGATTGAAGCAATCCAATCTTCTACCCTAATCAGAGGGCAGATT
129 CTCTTACCC-GACTATGGGGCAGATTGAAGCAATACAATCTTTTACCCTAACCAAAGGGCAGATT
*
460331 AAAGACCAATCGATCTCTTACCCTGACCATAGGGCAAATTGAAG
193 AAAGACCAATCGATCTCTTACCCCGACCATAGGGCAAATTGAAG
* * *
460375 CAATCCAATATTTTACCCTAACTAGAGGGTAGATTGAAGACCATCTGATCTCTTACCCCGACCAT
1 CAATCCAATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCAT
* *
460440 GGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACTAGAAGGCAGATTGAAGACCATCCGATCT
66 GGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAAGGCAAATTGAAGACCATCCGATCT
* * * * *
460505 CTTAGCCCGACCATGGGGCAGATTGAAGCAATTCAATTTTTTACCCTAACCAAAGGGCGGATTGA
131 CTTA-CCCGACTATGGGGCAGATTGAAGCAATACAATCTTTTACCCTAACCAAAGGGCAGATTAA
* * * * *
460570 AGACCATTCGATCTTTTACCCCGACGATGGGGCATATTGAAG
195 AGACCAATCGATCTCTTACCCCGACCATAGGGCAAATTGAAG
* * * * *
460612 CAATCCAATCTTTTACCCTAACTAGAGAGCAAATTAAAGACCATCCGATCTCTTATCCCAACCAT
1 CAATCCAATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCAT
* * **
460677 GGGGCAGATTGAAGTAATCCAAT-TTTTAACCCTAACCAGAAGGCAAATTGAAGACCATTTGATC
66 GGGGCAGATTGAAGAAATCCAATCTTTT-ACCCTAACTAGAAGGCAAATTGAAGACCATCCGATC
* *
460741 TCTTACCTCGACTATGGGGCAAATTGAAACAATACAATCTTTTACCC
130 TCTTACC-CGACTATGGGGCAGATTGAAGCAATACAATCTTTTACCC
460788 ATAAAGCTAT
Statistics
Matches: 360, Mismatches: 48, Indels: 10
0.86 0.11 0.02
Matches are distributed among these distances:
236 6 0.02
237 346 0.96
238 8 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (236 bp):
CAATCCAATCTTTTACCCTAACTAGAGGGCAAATTGAAGACCATCTGATCTCTTACCCCGACCAT
GGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAAGGCAAATTGAAGACCATCCGATCT
CTTACCCGACTATGGGGCAGATTGAAGCAATACAATCTTTTACCCTAACCAAAGGGCAGATTAAA
GACCAATCGATCTCTTACCCCGACCATAGGGCAAATTGAAG
Found at i:461300 original size:56 final size:56
Alignment explanation
Indices: 461214--461326 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
461204 GCGAAAGAGA
*
461214 GGGCTACTAAGAGAGAGACACCAGAAGATGAAATGCGGTGGGATTGCACAAAATTG
1 GGGCTACTAAGAGAGAGACACCAGAAGATGAAATACGGTGGGATTGCACAAAATTG
*
461270 GGGCTACTAAGAGAGAGACACCAGAAGATGAAATACGGTGGGATTGGACAAAATTG
1 GGGCTACTAAGAGAGAGACACCAGAAGATGAAATACGGTGGGATTGCACAAAATTG
461326 G
1 G
461327 TCTTTTTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.38, C:0.13, G:0.33, T:0.16
Consensus pattern (56 bp):
GGGCTACTAAGAGAGAGACACCAGAAGATGAAATACGGTGGGATTGCACAAAATTG
Found at i:462475 original size:29 final size:30
Alignment explanation
Indices: 462423--462638 Score: 151
Period size: 30 Copynumber: 7.3 Consensus size: 30
462413 TAAAATTATT
* *
462423 TTTGACCCTCGAAA-TTTCTAAAAATTAGAA
1 TTTGACCC-CCAAACTTTCCAAAAATTAGAA
462453 TTTGACCCCCAAACTTTCCAAAAATTAGAA
1 TTTGACCCCCAAACTTTCCAAAAATTAGAA
* * *
462483 TTTAACCCTCAAATTTTCC-AAAATTCA-AA
1 TTTGACCCCCAAACTTTCCAAAAATT-AGAA
** * *
462512 TTTGATTCCTAAACTTTCCAAAAATTTGAA
1 TTTGACCCCCAAACTTTCCAAAAATTAGAA
* * * **
462542 TTTGA-CCCTAAATTTTCTAAAAATCT-TTA
1 TTTGACCCCCAAACTTTCCAAAAAT-TAGAA
*
462571 TTTGACCCCTC-AACTTTCCAAAAATTTTG-A
1 TTTGACCCC-CAAACTTTCCAAAAA-TTAGAA
** * *
462601 TTTGACCCATAAAGTTTTCAAAAATTCA-AA
1 TTTGACCCCCAAACTTTCCAAAAATT-AGAA
462631 TTTGACCC
1 TTTGACCC
462639 AATTTTAATG
Statistics
Matches: 148, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
29 49 0.33
30 98 0.66
31 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (30 bp):
TTTGACCCCCAAACTTTCCAAAAATTAGAA
Found at i:462506 original size:59 final size:58
Alignment explanation
Indices: 462423--462638 Score: 226
Period size: 59 Copynumber: 3.6 Consensus size: 58
462413 TAAAATTATT
*
462423 TTTGACCCTCGAAA-TTTCTAAAAATT-AGAATTTGACCCCCAAACTTTCCAAAAATTAGAA
1 TTTGACCCT--AAATTTTC-AAAAATTCA-AATTTGACCCCCAAACTTTCCAAAAATTTGAA
* * ** *
462483 TTTAACCCTCAAATTTTCCAAAATTCAAATTTGATTCCTAAACTTTCCAAAAATTTGAA
1 TTTGACCCT-AAATTTTCAAAAATTCAAATTTGACCCCCAAACTTTCCAAAAATTTGAA
**
462542 TTTGACCCTAAATTTTCTAAAAA-TCTTTATTTGACCCCTC-AACTTTCCAAAAATTTTG-A
1 TTTGACCCTAAATTTTC-AAAAATTC-AAATTTGACCCC-CAAACTTTCCAAAAA-TTTGAA
462601 TTTGACCCATAAAGTTTTCAAAAATTCAAATTTGACCC
1 TTTGACCC-TAAA-TTTTCAAAAATTCAAATTTGACCC
462639 AATTTTAATG
Statistics
Matches: 131, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
58 10 0.08
59 79 0.60
60 35 0.27
61 7 0.05
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (58 bp):
TTTGACCCTAAATTTTCAAAAATTCAAATTTGACCCCCAAACTTTCCAAAAATTTGAA
Found at i:463669 original size:20 final size:20
Alignment explanation
Indices: 463640--463689 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
463630 AAATCAAATT
* *
463640 AAAATGATTTTAAACAAGTC
1 AAAATAATTTGAAACAAGTC
*
463660 AAAATAATTTGAACCAAGTC
1 AAAATAATTTGAAACAAGTC
*
463680 AAAATCATTT
1 AAAATAATTT
463690 CAACACATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (20 bp):
AAAATAATTTGAAACAAGTC
Found at i:468516 original size:109 final size:109
Alignment explanation
Indices: 468223--468516 Score: 354
Period size: 109 Copynumber: 2.7 Consensus size: 109
468213 AGTGATATAA
* * * * *
468223 ACCATCGCGTTGGCTGAGATCTTGCATATGTTACGGATTCTCGATAGCTTGTGTAAGCAGCATTG
1 ACCATCGCGATGGCTGAGATCTTGCCTAAGTTACGGATTCTCGATAGCTTGTGTGAGCAGCATCG
* * * *
468288 TGAGTTGGTGAATACTGAGTGGATACTATGTTCTGATGATACAT
66 TGAGTAGGTGAATACTAAATGGATACTACGTTCTGATGATACAT
* * * * * ** *
468332 ACCATCGCGATCGCTGAGATCTTACCTAAGTTACGGATTATCGACAGCTAGTGTGAAAAACATCG
1 ACCATCGCGATGGCTGAGATCTTGCCTAAGTTACGGATTCTCGATAGCTTGTGTGAGCAGCATCG
**
468397 TGAGCCGGTGAATACTAAATGGATACTACGTTCTGATGATACAT
66 TGAGTAGGTGAATACTAAATGGATACTACGTTCTGATGATACAT
* * * * * * *
468441 ACCGTCGCGATGGCTGAGATCTTGCCTAAGTTGCGAATTCTCAATAGCTTGTGTGAGCTGCACCA
1 ACCATCGCGATGGCTGAGATCTTGCCTAAGTTACGGATTCTCGATAGCTTGTGTGAGCAGCATCG
468506 TGAGTAGGTGA
66 TGAGTAGGTGA
468517 TATAGACCGT
Statistics
Matches: 150, Mismatches: 35, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
109 150 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (109 bp):
ACCATCGCGATGGCTGAGATCTTGCCTAAGTTACGGATTCTCGATAGCTTGTGTGAGCAGCATCG
TGAGTAGGTGAATACTAAATGGATACTACGTTCTGATGATACAT
Done.