Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008026.1 Hibiscus syriacus cultivar Beakdansim tig00110502_pilon, 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: 525378
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 3 of 4
Found at i:362956 original size:22 final size:22
Alignment explanation
Indices: 362928--362987 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
362918 TTTTTCTTTA
362928 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTTCCCTCCTGT
362950 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTTCCCTCCTGT
362972 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
362988 CTATGAGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.10, C:0.27, G:0.38, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTCCTGT
Found at i:366584 original size:23 final size:23
Alignment explanation
Indices: 366558--366626 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
366548 CACCACAGCT
*
366558 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
366581 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
366604 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
366627 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:366809 original size:101 final size:100
Alignment explanation
Indices: 366645--366845 Score: 323
Period size: 101 Copynumber: 2.0 Consensus size: 100
366635 TGTCCTAAGG
*
366645 ACCACATATCACTCCTTAAGAATCATATACATATACTAGGATCAAGTATGTGTCTCAACAGACTT
1 ACCACATATCACTCCTTAAGAATCA-ATACATATACAAGGATCAAGTATGTGTCTCAACAGACTT
366710 CACACATGTTCCAAAGAATACATATATGTCCCGAAGA
65 CACACATGTTCCAAAG-ATACATATATGTCCCGAAGA
* * *
366747 ACCACATATCATTCCTTAAGAATC-ATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTT
1 ACCACATATCACTCCTTAAGAATCAATACATAT-ACAAGGATCAAGTATGTGTCTCAACAGACTT
*
366811 CATACATGTTCCAAAGATACATATATGTCCCGAAG
65 CACACATGTTCCAAAGATACATATATGTCCCGAAG
366846 GACCGCGTAG
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
100 27 0.29
101 43 0.46
102 23 0.25
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (100 bp):
ACCACATATCACTCCTTAAGAATCAATACATATACAAGGATCAAGTATGTGTCTCAACAGACTTC
ACACATGTTCCAAAGATACATATATGTCCCGAAGA
Found at i:370221 original size:12 final size:12
Alignment explanation
Indices: 370201--370234 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
370191 CATTGATGCA
370201 CTACAGTAATTG
1 CTACAGTAATTG
*
370213 CTACCGTAA-TG
1 CTACAGTAATTG
370224 CTACAGTAATT
1 CTACAGTAATT
370235 TCAGCATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (12 bp):
CTACAGTAATTG
Found at i:370607 original size:42 final size:42
Alignment explanation
Indices: 370560--370720 Score: 186
Period size: 42 Copynumber: 3.8 Consensus size: 42
370550 TAACAAATAT
370560 TTTACCATTATTAACCATAAGCTCGTAAGC-T-TTTTACCAAAA
1 TTTACCATTATT--CCATAAGCTCGTAAGCTTATTTTACCAAAA
* * *
370602 TTTACCATTGTACC-TAAGCTCGTAAGCTTATTTTACCAATA
1 TTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAA
* * * *
370643 CTTACCATTATTCCATAAGCCCATAAGCTTATTTTACCCATATAC
1 TTTACCATTATTCCATAAGCTCGTAAGCTTATTTTA-CCA-A-AA
370688 TTT-CCATTATTCCATAAGCTCGTAAGCTTATTT
1 TTTACCATTATTCCATAAGCTCGTAAGCTTATTT
370721 GCATGCTTAC
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
39 13 0.13
40 3 0.03
41 21 0.21
42 29 0.29
43 3 0.03
44 29 0.29
45 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (42 bp):
TTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAA
Found at i:370703 original size:44 final size:42
Alignment explanation
Indices: 370561--370720 Score: 164
Period size: 44 Copynumber: 3.8 Consensus size: 42
370551 AACAAATATT
* * * *
370561 TTACCATTATTAACCATAAGCTCGTAAGC-T-TTTTACCAAAAT
1 TTACCATTATT--CCATAAGCCCATAAGCTTATTTTACCAATAC
* * * *
370603 TTACCATTGTACC-TAAGCTCGTAAGCTTATTTTACCAATAC
1 TTACCATTATTCCATAAGCCCATAAGCTTATTTTACCAATAC
370644 TTACCATTATTCCATAAGCCCATAAGCTTATTTTACCCATATAC
1 TTACCATTATTCCATAAGCCCATAAGCTTATTTTA-CCA-ATAC
* * *
370688 TTTCCATTATTCCATAAGCTCGTAAGCTTATTT
1 TTACCATTATTCCATAAGCCCATAAGCTTATTT
370721 GCATGCTTAC
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
39 13 0.13
40 3 0.03
41 21 0.21
42 28 0.27
43 3 0.03
44 34 0.33
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (42 bp):
TTACCATTATTCCATAAGCCCATAAGCTTATTTTACCAATAC
Found at i:370830 original size:22 final size:21
Alignment explanation
Indices: 370805--370849 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
370795 GGTATACGAG
370805 TAAAATACCTGCACCGTAGTGC
1 TAAAA-ACCTGCACCGTAGTGC
*
370827 T--AAACCTGCACCGTAGTGG
1 TAAAAACCTGCACCGTAGTGC
370846 TAAA
1 TAAA
370850 CCTACACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
19 16 0.80
20 2 0.10
21 1 0.05
22 1 0.05
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
TAAAAACCTGCACCGTAGTGC
Found at i:370835 original size:19 final size:19
Alignment explanation
Indices: 370811--370852 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
370801 CGAGTAAAAT
370811 ACCTGCACCGTAGTGCTAA
1 ACCTGCACCGTAGTGCTAA
*
370830 ACCTGCACCGTAGTGGTAA
1 ACCTGCACCGTAGTGCTAA
370849 ACCT
1 ACCT
370853 ACACTAAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (19 bp):
ACCTGCACCGTAGTGCTAA
Found at i:373538 original size:18 final size:18
Alignment explanation
Indices: 373515--373562 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
373505 CCTATGGTCA
373515 AGTATTGATACCCCTATG
1 AGTATTGATACCCCTATG
373533 AGTATTGATACCCCTATG
1 AGTATTGATACCCCTATG
373551 AGTATTGATACC
1 AGTATTGATACC
373563 AAAAATGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (18 bp):
AGTATTGATACCCCTATG
Found at i:374393 original size:84 final size:83
Alignment explanation
Indices: 374253--374420 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 83
374243 AGATGAGTGA
374253 AATAAAGGGCTCATCTTTGTAAAATGGGGAAAATCACACTATAGGTCATTCCTCATCTTTTTAAA
1 AATAAAGGGCTCATCTTTGTAAAATGGGGAAAATCACACTATAGGTCATTCCTCATCTTTTTAAA
374318 TTCAAAAATCTCCTTTTG
66 TTCAAAAATCTCCTTTTG
374336 AATAAAGGGCTCATCTTTGTAAAAATGGGGAAAATCACACTATAGGTCATTCCTCATCTTTTTAA
1 AATAAAGGGCTCATCTTTGT-AAAATGGGGAAAATCACACTATAGGTCATTCCTCATCTTTTTAA
374401 ATTCAAAAATCTCCTTTTG
65 ATTCAAAAATCTCCTTTTG
374420 A
1 A
374421 TGACTAAATG
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 20 0.24
84 64 0.76
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (83 bp):
AATAAAGGGCTCATCTTTGTAAAATGGGGAAAATCACACTATAGGTCATTCCTCATCTTTTTAAA
TTCAAAAATCTCCTTTTG
Found at i:374441 original size:33 final size:33
Alignment explanation
Indices: 374399--374464 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
374389 TCATCTTTTT
374399 AAATTCAAAAATCTCCTTTTGATGACTAAATGG
1 AAATTCAAAAATCTCCTTTTGATGACTAAATGG
374432 AAATTCAAAAATCTCCTTTTGATGACTAAATGG
1 AAATTCAAAAATCTCCTTTTGATGACTAAATGG
374465 GCTAAATTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
AAATTCAAAAATCTCCTTTTGATGACTAAATGG
Found at i:378318 original size:23 final size:23
Alignment explanation
Indices: 378288--378333 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
378278 TTATATTTTT
*
378288 ACAATAATATTATTTTTTTCATC
1 ACAATAATACTATTTTTTTCATC
378311 ACAATAATACTATTTTTTTCATC
1 ACAATAATACTATTTTTTTCATC
378334 CAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (23 bp):
ACAATAATACTATTTTTTTCATC
Found at i:379543 original size:55 final size:56
Alignment explanation
Indices: 379456--379608 Score: 245
Period size: 55 Copynumber: 2.8 Consensus size: 56
379446 TTTGGGCTCT
* *
379456 TATTTTTATGCTTCTTAATGGCAACAATTGATAGATATATTCGATTTCGGGACCCC
1 TATTTTTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGGGACCCC
*
379512 TATTTTTATGTTTCTTAAT-GCAACAACTGATAGATATACTCGATTTCGGGACCCC
1 TATTTTTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGGGACCCC
* * *
379567 TACTTTTATGCTTATTAATGGCAACAACTAATAGATATACTC
1 TATTTTTATGCTTCTTAATGGCAACAACTGATAGATATACTC
379609 AATTCTGATG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 50 0.56
56 39 0.44
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (56 bp):
TATTTTTATGCTTCTTAATGGCAACAACTGATAGATATACTCGATTTCGGGACCCC
Found at i:379629 original size:55 final size:55
Alignment explanation
Indices: 379456--379665 Score: 230
Period size: 55 Copynumber: 3.8 Consensus size: 55
379446 TTTGGGCTCT
* * * *
379456 TATTTTTATGCTTCTTAATGGCAACAATTGATAGATATATTCGATTTCGGGACCCC
1 TATTTTTATGCTTATTAAT-GCAACAACTAATAGATATACTCGATTTCGGGACCCC
* * *
379512 TATTTTTATGTTTCTTAATGCAACAACTGATAGATATACTCGATTTCGGGACCCC
1 TATTTTTATGCTTATTAATGCAACAACTAATAGATATACTCGATTTCGGGACCCC
* * * * **
379567 TACTTTTATGCTTATTAATGGCAACAACTAATAGATATACTC-AATTC-TGATGCTT
1 TATTTTTATGCTTATTAAT-GCAACAACTAATAGATATACTCGATTTCGGGA-CCCC
* *
379622 TATTTTTATGCTTATTAAT--AATAACTAATAAATATACTCGATTT
1 TATTTTTATGCTTATTAATGCAACAACTAATAGATATACTCGATTT
379666 TAAAGCCCTA
Statistics
Matches: 135, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
52 18 0.13
53 3 0.02
54 2 0.01
55 73 0.54
56 39 0.29
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (55 bp):
TATTTTTATGCTTATTAATGCAACAACTAATAGATATACTCGATTTCGGGACCCC
Found at i:382184 original size:20 final size:19
Alignment explanation
Indices: 382143--382190 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
382133 AATAAATCAA
* *
382143 AAATAATAATTTAACTACT
1 AAATAATAATTTAACCAAT
*
382162 AAATAGATAATTTATCCAAT
1 AAATA-ATAATTTAACCAAT
382182 AAATTAATA
1 AAA-TAATA
382191 TTTTTTTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.21
20 17 0.71
21 2 0.08
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
AAATAATAATTTAACCAAT
Found at i:388300 original size:23 final size:19
Alignment explanation
Indices: 388254--388305 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 19
388244 TGTAAAAATG
*
388254 GTATCGGTACCTAAGGGGA
1 GTATCGATACCTAAGGGGA
388273 GTATCGATACCATAAGAGGGTA
1 GTATCGATACC-TAAG-GGG-A
388295 GTTATCGATAC
1 G-TATCGATAC
388306 TATAGTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.36
20 4 0.14
21 3 0.11
22 2 0.07
23 9 0.32
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (19 bp):
GTATCGATACCTAAGGGGA
Found at i:389482 original size:15 final size:15
Alignment explanation
Indices: 389462--389504 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
389452 AGCATTATAT
389462 GTTATGTGATATGAA
1 GTTATGTGATATGAA
389477 GTTATGTGATATGAA
1 GTTATGTGATATGAA
389492 GTTATGTGATATG
1 GTTATGTGATATG
389505 TGTTATAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (15 bp):
GTTATGTGATATGAA
Found at i:389736 original size:21 final size:21
Alignment explanation
Indices: 389710--389752 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
389700 TCGAGGGTTC
*
389710 TATGTGGTCCTTTGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
389731 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
389752 T
1 T
389753 CCTATGTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:391285 original size:27 final size:28
Alignment explanation
Indices: 391254--391307 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
391244 CGAATTATCA
*
391254 TTAACCG-AATTAACCAAACTTTTTTCT
1 TTAACCGTAATCAACCAAACTTTTTTCT
391281 TTAACCGTTAATCAACCAAACTTTTTT
1 TTAACCG-TAATCAACCAAACTTTTTT
391308 TGAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
29 17 0.71
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (28 bp):
TTAACCGTAATCAACCAAACTTTTTTCT
Found at i:392257 original size:31 final size:30
Alignment explanation
Indices: 392222--392316 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
392212 AAAATAATTG
392222 AAGTACTTAAAGTGATTACATATAATAGTTT
1 AAGTACTTAAAGT-ATTACATATAATAGTTT
* * *
392253 AAGTAAC-T--AGT-TTGACCAAAAAATA-TTG
1 AAGT-ACTTAAAGTATT-A-CATATAATAGTTT
392281 AAGTACTTAAAGTAATTACATATAATAGTTT
1 AAGTACTTAAAGT-ATTACATATAATAGTTT
392312 AAGTA
1 AAGTA
392317 ACTAGTTTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
27 4 0.08
28 8 0.16
29 10 0.20
30 10 0.20
31 13 0.27
32 4 0.08
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (30 bp):
AAGTACTTAAAGTATTACATATAATAGTTT
Found at i:392290 original size:59 final size:60
Alignment explanation
Indices: 392203--392337 Score: 238
Period size: 59 Copynumber: 2.3 Consensus size: 60
392193 GAGATTTTTT
* *
392203 TTTGACAAAAAAATAATTGAAGTACTTAAAGTGATTACATATAATAGTTTAAGTAACTAG
1 TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
392263 TTTGACCAAAAAAT-ATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
1 TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
392322 TTTGACC-AAAAATAAT
1 TTTGACCAAAAAATAAT
392338 AATTTAGTTA
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
58 6 0.08
59 53 0.74
60 13 0.18
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (60 bp):
TTTGACCAAAAAATAATTGAAGTACTTAAAGTAATTACATATAATAGTTTAAGTAACTAG
Found at i:392337 original size:31 final size:31
Alignment explanation
Indices: 392243--392343 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 31
392233 GTGATTACAT
392243 ATAATAGTTTAAGTAACTAGTTTGACC-AAA
1 ATAATAGTTTAAGTAACTAGTTTGACCAAAA
* *** * ** * *
392273 A-AATA-TTGAAGT-ACTTAAAGTAATTACAT
1 ATAATAGTTTAAGTAAC-TAGTTTGACCAAAA
392302 ATAATAGTTTAAGTAACTAGTTTGACCAAAA
1 ATAATAGTTTAAGTAACTAGTTTGACCAAAA
*
392333 ATAATAATTTA
1 ATAATAGTTTA
392344 GTTATCTAAA
Statistics
Matches: 47, Mismatches: 19, Indels: 9
0.63 0.25 0.12
Matches are distributed among these distances:
27 2 0.04
28 10 0.21
29 6 0.13
30 5 0.11
31 22 0.47
32 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (31 bp):
ATAATAGTTTAAGTAACTAGTTTGACCAAAA
Found at i:396289 original size:6 final size:6
Alignment explanation
Indices: 396278--396305 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
396268 GTGAAGGGGG
396278 GAAATT GAAATT GAAATT GAAATT GAAA
1 GAAATT GAAATT GAAATT GAAATT GAAA
396306 CCGTTGATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.29
Consensus pattern (6 bp):
GAAATT
Found at i:398072 original size:25 final size:25
Alignment explanation
Indices: 398044--398106 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
398034 CCGATTCTTG
398044 ACTTTATAAATACAACATATGATTT
1 ACTTTATAAATACAACATATGATTT
* * *
398069 ACTTTTTTTATTA-AACATATGATTT
1 AC-TTTATAAATACAACATATGATTT
398094 AC-TTATAAATACA
1 ACTTTATAAATACA
398107 TAAAGTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 6 0.20
24 1 0.03
25 16 0.53
26 7 0.23
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (25 bp):
ACTTTATAAATACAACATATGATTT
Found at i:401511 original size:55 final size:55
Alignment explanation
Indices: 401374--401630 Score: 360
Period size: 55 Copynumber: 4.7 Consensus size: 55
401364 GTACTATAGA
* *
401374 CACTTTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCATACA-G
1 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGG
* *
401428 CACTTCATGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGG
1 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGG
* *
401483 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAGAGG
1 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGG
*
401538 CACTTCTTGTGCATATTCACGGAATTCATCATGAGTTGATG-ATCACCATACAGG
1 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGG
* * *** *
401592 TACTAT-GTGTACA-GCCCACGAAATTCATCATGAGTTGAT
1 CACT-TCGTGTGCATATTCACGGAATTCATCATGAGTTGAT
401631 AAATTCTCGT
Statistics
Matches: 185, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
53 22 0.12
54 68 0.37
55 95 0.51
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (55 bp):
CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGG
Found at i:401583 original size:109 final size:108
Alignment explanation
Indices: 401378--401630 Score: 366
Period size: 109 Copynumber: 2.3 Consensus size: 108
401368 TATAGACACT
*
401378 TTGTGTGCATATTCACAGAATTCATCATGAGTTGATGAATCACCATACAGCACTTCATGTGCATA
1 TTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGCACTTCATGTGCATA
*
401443 TTCACGGAATTCATCATGAGTTGATGAATCACCGTACAGGCAC
66 TTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCAC
* * *
401486 TTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAGAGGCACTTCTTGTGCA
1 TT-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACA-GCACTTCATGTGCA
*
401551 TATTCACGGAATTCATCATGAGTTGATG-ATCACCATACAGGTAC
64 TATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCAC
* *** *
401595 TATGTGTACA-GCCCACGAAATTCATCATGAGTTGAT
1 T-TGTGTGCATATTCACGGAATTCATCATGAGTTGAT
401631 AAATTCTCGT
Statistics
Matches: 131, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
108 24 0.18
109 65 0.50
110 42 0.32
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (108 bp):
TTGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGCACTTCATGTGCATA
TTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCAC
Found at i:403605 original size:26 final size:27
Alignment explanation
Indices: 403564--403616 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
403554 TGTTTTTTCT
403564 AGTTGACCCCTGGTTCTTCATATCATA
1 AGTTGACCCCTGGTTCTTCATATCATA
403591 AGTTGA-CCCTGGTTCTTCATATCATA
1 AGTTGACCCCTGGTTCTTCATATCATA
403617 TATTAGTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (27 bp):
AGTTGACCCCTGGTTCTTCATATCATA
Found at i:408054 original size:94 final size:94
Alignment explanation
Indices: 407903--408087 Score: 237
Period size: 94 Copynumber: 2.0 Consensus size: 94
407893 TATTGATGAG
* * * *
407903 GTAGTATCGATACCATGATAAGGGGTATCGATACAAAACAACTTCAAATCTAATTTTGGTATTGA
1 GTAGTATCGATACCATGATAAGAGGTATCGATACAAAACAACATCAAACCTAATTTTGGTATCGA
** * *
407968 TACCGGTAGGGGGTATCGGTACCATAGAGA
66 TACC-CAAAGGGATATCGGTACCATAGAGA
* * * * *
407998 GTAGTATCGATACCATGGTAA-AGGTATCGATACCAAGCAACATCTAACCTATTTTTGGTATCGA
1 GTAGTATCGATACCATGATAAGAGGTATCGATACAAAACAACATCAAACCTAATTTTGGTATCGA
408062 TACCCAAAGGGATATCGGTACCATAG
66 TACCCAAAGGGATATCGGTACCATAG
408088 TATAGAAGTA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
93 18 0.23
94 39 0.51
95 20 0.26
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (94 bp):
GTAGTATCGATACCATGATAAGAGGTATCGATACAAAACAACATCAAACCTAATTTTGGTATCGA
TACCCAAAGGGATATCGGTACCATAGAGA
Found at i:408098 original size:94 final size:94
Alignment explanation
Indices: 407905--408124 Score: 228
Period size: 94 Copynumber: 2.3 Consensus size: 94
407895 TTGATGAGGT
* * * * *
407905 AGTATCGATACCATGATAAGGGGTATCGATACAAAACAACTTCAAATCTAATTTTGGTATTGATA
1 AGTATCGATACCATGGTAA-AGGTATCGATACAAAACAACATCAAACCTAATTTTGGTATCGATA
** * * *
407970 CCGGTAGGGGGTATCGGTACCATAGAGAGT
65 CCGCAAAGGGATATCGGTACCATAGAGAGA
* * * *
408000 AGTATCGATACCATGGTAAAGGTATCGATACCAAGCAACATCTAACCTATTTTTGGTATCGATAC
1 AGTATCGATACCATGGTAAAGGTATCGATACAAAACAACATCAAACCTAATTTTGGTATCGATAC
*
408065 C-CAAAGGGATATCGGTACCATAGTATAGA
66 CGCAAAGGGATATCGGTACCATAG-AGAGA
* * * *
408094 AGTATTGGTACCAGGGTAGTA-GTATCGATAC
1 AGTATCGATACCATGGTA-AAGGTATCGATAC
408125 TATGTAGACA
Statistics
Matches: 104, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
93 18 0.17
94 67 0.64
95 19 0.18
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (94 bp):
AGTATCGATACCATGGTAAAGGTATCGATACAAAACAACATCAAACCTAATTTTGGTATCGATAC
CGCAAAGGGATATCGGTACCATAGAGAGA
Found at i:408480 original size:56 final size:55
Alignment explanation
Indices: 408336--408542 Score: 240
Period size: 55 Copynumber: 3.8 Consensus size: 55
408326 TTTTTGAATG
* ** *
408336 CTTCATGTGCATATTCACATAATTTATCATGAGTTGATGAATCACCATACAGGCA
1 CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCA
* * *
408391 CTTCGTGTGCATATTCACGGAATTCATCTTGAGTTAATGAATCACCATACATGCA
1 CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCA
* *
408446 CTTCTTTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTAC-GGACA
1 CTTC-GTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGG-CA
* *** *
408502 CTAT-GTGTACA-GCCCACGGAATTCATCATGAGTCGATGAAT
1 CT-TCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT
408543 TCTCGTATAG
Statistics
Matches: 131, Mismatches: 18, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
54 26 0.20
55 58 0.44
56 46 0.35
57 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (55 bp):
CTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCATACAGGCA
Found at i:414595 original size:32 final size:31
Alignment explanation
Indices: 414559--414666 Score: 82
Period size: 32 Copynumber: 3.5 Consensus size: 31
414549 ACTTGTATAG
*
414559 GAGCCAACCTAAGGTAATGA-CTT-GGAGCCTTA
1 GAGCCAACCCAAGG-AAT-ACCTTAGG-GCCTTA
*
414591 GAGCCTACCCAAGGAATACCTTAGGGCCTTA
1 GAGCCAACCCAAGGAATACCTTAGGGCCTTA
* * *
414622 GAG---ACTCAAGAAAGCACCTTAGGGCCTTA
1 GAGCCAACCCAAGGAA-TACCTTAGGGCCTTA
* *
414651 GATCCTACCCAAGGAA
1 GAGCCAACCCAAGGAA
414667 GCACCTTGGG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
28 8 0.13
29 16 0.26
30 1 0.02
31 15 0.24
32 22 0.35
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (31 bp):
GAGCCAACCCAAGGAATACCTTAGGGCCTTA
Found at i:415719 original size:34 final size:32
Alignment explanation
Indices: 415680--415749 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
415670 TTTTGTAAAG
* *
415680 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
415714 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
415746 GGGA
1 GGGA
415750 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:418355 original size:16 final size:16
Alignment explanation
Indices: 418334--418372 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
418324 GAGACAACCA
418334 ATTTTTACTATTTTTT
1 ATTTTTACTATTTTTT
* *
418350 ATTTTTATTTTTTTTT
1 ATTTTTACTATTTTTT
418366 ATATTTT
1 AT-TTTT
418373 TAGGTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTACTATTTTTT
Found at i:419342 original size:21 final size:21
Alignment explanation
Indices: 419318--419441 Score: 67
Period size: 21 Copynumber: 5.9 Consensus size: 21
419308 ACTTTGACTA
*
419318 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
* * *
419339 TCGCGTTGTGATTTATTTCAAGT
1 TCGCGTTGCGA--TAGTCCAAGT
* *
419362 T--CGTTGCAATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
419381 TCGCGTTGCGATTTATTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
* * * **
419404 T--TGTTACGATACTAGAAGT
1 TCGCGTTGCGATAGTCCAAGT
419423 TCGCGTTGCGATAGTCCAA
1 TCGCGTTGCGATAGTCCAA
419442 AATCGCAACG
Statistics
Matches: 71, Mismatches: 24, Indels: 16
0.64 0.22 0.14
Matches are distributed among these distances:
19 15 0.21
21 39 0.55
23 17 0.24
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:419422 original size:42 final size:42
Alignment explanation
Indices: 419335--419434 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
419325 GCGATAGTCC
* * * * * *
419335 AAGTTCGCGTTGTGATTTATTTCAAGTTCGTTGCAATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTACAATACTAG
* *
419377 AAGTTCGCGTTGCGATTTATTCCAAATTTGTTACGATACTAG
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTACAATACTAG
419419 AAGTTCGCGTTGCGAT
1 AAGTTCGCGTTGCGAT
419435 AGTCCAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAATTCGTTACAATACTAG
Found at i:420233 original size:21 final size:21
Alignment explanation
Indices: 420181--420263 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
420171 CGTTGCAATT
*
420181 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
* *
420200 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
420223 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
420244 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
420264 TATGTAAATC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.11
21 40 0.71
23 10 0.18
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:420302 original size:21 final size:21
Alignment explanation
Indices: 420272--420448 Score: 172
Period size: 21 Copynumber: 8.5 Consensus size: 21
420262 AATATGTAAA
*
420272 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
420293 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
420313 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
*
420334 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
420355 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
420375 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
*
420396 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
420417 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
420438 TCGCGTTGCGA
1 TCGCATTGCGA
420449 ATCTAGAAAC
Statistics
Matches: 132, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
20 34 0.26
21 96 0.73
22 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:420470 original size:62 final size:62
Alignment explanation
Indices: 420272--420434 Score: 308
Period size: 62 Copynumber: 2.6 Consensus size: 62
420262 AATATGTAAA
* *
420272 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
420334 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
420396 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
420435 AGTTCGCGTT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 99 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (62 bp):
TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
Found at i:421532 original size:14 final size:15
Alignment explanation
Indices: 421513--421552 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
421503 TTGAACATTA
*
421513 CAGAAAAATTC-GAG
1 CAGAAAAATACAGAG
421527 CAGAAAAATACAGAG
1 CAGAAAAATACAGAG
421542 CAGGAAAAATA
1 CA-GAAAAATA
421553 GTTTGGTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 5 0.22
16 8 0.35
ACGTcount: A:0.57, C:0.12, G:0.20, T:0.10
Consensus pattern (15 bp):
CAGAAAAATACAGAG
Found at i:422488 original size:24 final size:24
Alignment explanation
Indices: 422457--422536 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 24
422447 AACAATTATG
422457 GGAATTATCTTTTGCAATTTATTA
1 GGAATTATCTTTTGCAATTTATTA
* *
422481 GGGATTATCTTTTGTAATTT-TTA
1 GGAATTATCTTTTGCAATTTATTA
* * *
422504 GAAATTATCTTCT-CAATTTTTTA
1 GGAATTATCTTTTGCAATTTATTA
*
422527 AGAATTATCT
1 GGAATTATCT
422537 CTTAGGATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 5 0.11
23 24 0.51
24 18 0.38
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (24 bp):
GGAATTATCTTTTGCAATTTATTA
Found at i:422503 original size:26 final size:26
Alignment explanation
Indices: 422451--422500 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
422441 ATTTCAAACA
422451 ATTATGGGAATTATCTTTTGCAATTT
1 ATTATGGGAATTATCTTTTGCAATTT
*
422477 ATTA-GGG-ATTATCTTTTGTAATTT
1 ATTATGGGAATTATCTTTTGCAATTT
422501 TTAGAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
25 3 0.13
26 4 0.17
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (26 bp):
ATTATGGGAATTATCTTTTGCAATTT
Found at i:422698 original size:20 final size:20
Alignment explanation
Indices: 422652--422693 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
422642 TTCTTCAATA
*
422652 AAGTTTTTACTTTTCTTTTT
1 AAGTTTTTACTTTTCCTTTT
422672 AAGTTTTTACTTTTCGCTTTT
1 AAGTTTTTACTTTTC-CTTTT
422693 A
1 A
422694 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (20 bp):
AAGTTTTTACTTTTCCTTTT
Found at i:422738 original size:26 final size:26
Alignment explanation
Indices: 422709--422760 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
422699 ATTTTAAAAT
422709 GCTAAGTATAATTTCTATAATACTTA
1 GCTAAGTATAATTTCTATAATACTTA
*
422735 GCTAAGTATGATTTCTATAATACTTA
1 GCTAAGTATAATTTCTATAATACTTA
422761 TCTACGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (26 bp):
GCTAAGTATAATTTCTATAATACTTA
Found at i:423703 original size:2 final size:2
Alignment explanation
Indices: 423696--423734 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
423686 TCTCTTTAAA
423696 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 A
423735 CCCCTCTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:423871 original size:3 final size:3
Alignment explanation
Indices: 423863--423912 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
423853 TTTAATATAG
* * *
423863 ATT ATT ATT ATT -TT -TT ATT GTT ATT ATT AAT A-T ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
423908 ATT AT
1 ATT AT
423913 CATTTACTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:425721 original size:2 final size:2
Alignment explanation
Indices: 425714--425746 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
425704 ATTATTTACT
425714 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
425747 TTATTAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:430067 original size:17 final size:19
Alignment explanation
Indices: 430020--430072 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 19
430010 AAAAGAATGT
430020 ATACTCTTTGATTATTTATAA
1 ATACT-TTT-ATTATTTATAA
430041 ATA-TTATTATT-TTTA-AA
1 ATACTT-TTATTATTTATAA
430058 ATACTTTTATTATTT
1 ATACTTTTATTATTT
430073 CACATTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 10 0.34
18 9 0.31
19 4 0.14
20 3 0.10
21 3 0.10
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (19 bp):
ATACTTTTATTATTTATAA
Found at i:434035 original size:3 final size:3
Alignment explanation
Indices: 434027--434127 Score: 202
Period size: 3 Copynumber: 33.7 Consensus size: 3
434017 AACTCATGTG
434027 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
434075 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
434123 CTT CT
1 CTT CT
434128 CCTCCATAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:440621 original size:30 final size:31
Alignment explanation
Indices: 440562--440628 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
440552 CATTACTTAC
* *
440562 GTACATGTACCATGAGTCATATCATCATTTAT
1 GTACATGTA-CATGAGTCACATAATCATTTAT
*
440594 GTACATGT-CATGTGTCACATAATCATTTAT
1 GTACATGTACATGAGTCACATAATCATTTAT
440624 GTACA
1 GTACA
440629 CATGACCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 24 0.75
32 8 0.25
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (31 bp):
GTACATGTACATGAGTCACATAATCATTTAT
Found at i:441215 original size:117 final size:117
Alignment explanation
Indices: 440994--441217 Score: 292
Period size: 117 Copynumber: 1.9 Consensus size: 117
440984 TATACCGTTT
*
440994 ATTTATTCAAAATTGAATGAATAAACAAGAGAAATGAAAAAAGAGGATAAAAAACTAAACATTTT
1 ATTTATTCAAAATTGAATGAATAAACAAGAGAAATGAAAAAAGAGGATAAAAAACTAAAAATTTT
* * **
441059 ATGATATTATAAAAATTAGAGGTCCTAATTATAAATATAAAAAATTGATTAA
66 ACGAAATTATAAAAATTAGAGACCCTAATTATAAATATAAAAAATTGATTAA
* * * * *
441111 ATTTAATTTAAAATTGAATGAATTAATAAGAGAAATGTAAAAAGAGGA-CAAAAACTAAAAATTT
1 ATTT-ATTCAAAATTGAATGAATAAACAAGAGAAATGAAAAAAGAGGATAAAAAACTAAAAATTT
* *
441175 TACGAAATTCA-AAAAATTAG-GAACCCTATTTATAAGTATAAAA
65 TACGAAATT-ATAAAAATTAGAG-ACCCTAATTATAAATATAAAA
441218 TTGGGGGGCT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
116 1 0.01
117 51 0.55
118 40 0.43
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (117 bp):
ATTTATTCAAAATTGAATGAATAAACAAGAGAAATGAAAAAAGAGGATAAAAAACTAAAAATTTT
ACGAAATTATAAAAATTAGAGACCCTAATTATAAATATAAAAAATTGATTAA
Found at i:443184 original size:12 final size:13
Alignment explanation
Indices: 443157--443191 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
443147 TAAAATATTT
443157 AAAATTATAATAA
1 AAAATTATAATAA
*
443170 AAAATTATGAT-A
1 AAAATTATAATAA
443182 AAAATTATAA
1 AAAATTATAA
443192 ATTAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AAAATTATAATAA
Found at i:444162 original size:2 final size:2
Alignment explanation
Indices: 444157--444198 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
444147 AAAAAATTGA
* * *
444157 AT AT AT AT AT AT AT AT AT AT AT A- AG AC AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
444198 A
1 A
444199 GTTTATATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:444402 original size:9 final size:9
Alignment explanation
Indices: 444388--444427 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
444378 GTGTAAACAA
444388 TATATAAAT
1 TATATAAAT
*
444397 TATATAAAG
1 TATATAAAT
444406 TAT-TAAAT
1 TATATAAAT
*
444414 TATATAATT
1 TATATAAAT
444423 TATAT
1 TATAT
444428 TAATATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATAAAT
Found at i:444428 original size:19 final size:20
Alignment explanation
Indices: 444406--444460 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
444396 TTATATAAAG
444406 TATTAAATTATATAA-TTTA
1 TATTAAATTATATAAGTTTA
*
444425 TATTAATATAATATAAGTTTA
1 TATTAA-ATTATATAAGTTTA
*
444446 TATATAAACTATATA
1 TAT-TAAATTATATA
444461 TATAAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 6 0.20
20 8 0.27
21 13 0.43
22 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TATTAAATTATATAAGTTTA
Found at i:444460 original size:13 final size:13
Alignment explanation
Indices: 444444--444529 Score: 64
Period size: 13 Copynumber: 6.1 Consensus size: 13
444434 AATATAAGTT
444444 TATATATAAACTA
1 TATATATAAACTA
444457 TATATATAAACTA
1 TATATATAAACTA
444470 TATAATTAATATAAGCTA
1 TAT-A-T-ATA-AA-CTA
* *
444488 TACATATAAATTA
1 TATATATAAACTA
* * *
444501 TGTTTATATGAACCA
1 --TATATATAAACTA
444516 TATATATAAACTA
1 TATATATAAACTA
444529 T
1 T
444530 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
13 29 0.52
14 3 0.05
15 12 0.21
16 4 0.07
17 3 0.05
18 5 0.09
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:444534 original size:2 final size:2
Alignment explanation
Indices: 444529--444559 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
444519 ATATAAACTA
*
444529 TG TG TG TG TG TG TT TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
444560 TATGTGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:444636 original size:2 final size:2
Alignment explanation
Indices: 444629--444710 Score: 91
Period size: 2 Copynumber: 42.0 Consensus size: 2
444619 ATATTAACAT
*
444629 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
444671 CTA -A TA TA -A GTA -A TC TA TA AA T- TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
444711 GTTTATAGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
1 4 0.06
2 62 0.91
3 2 0.03
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:445016 original size:35 final size:36
Alignment explanation
Indices: 444948--445021 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
444938 ACAATAGTTA
*
444948 ATATATGTAACCTATAGTATATGTATACATATAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
444985 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
445020 AT
1 AT
445022 GTATACTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:445098 original size:2 final size:2
Alignment explanation
Indices: 445023--445089 Score: 82
Period size: 2 Copynumber: 33.0 Consensus size: 2
445013 ATAAACTATG
*
445023 TA TA CTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
445067 TA TA -A CA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
445090 AACTATATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.02
2 53 0.93
3 3 0.05
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:445323 original size:35 final size:36
Alignment explanation
Indices: 445255--445328 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
445245 ATAATAGTTA
*
445255 ATATATGTAACCTATAGTATATGTATACATATAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
445292 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
445327 AT
1 AT
445329 GTATAGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:445337 original size:20 final size:20
Alignment explanation
Indices: 445314--445361 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
445304 TATAGTACAT
* *
445314 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
445334 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
445354 -TATATATA
1 GTATATATA
445362 TATATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:445379 original size:280 final size:298
Alignment explanation
Indices: 444884--445665 Score: 927
Period size: 308 Copynumber: 2.6 Consensus size: 298
444874 ATATAGTTTA
*
444884 TATAAACAATAGTTCATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAA
1 TATAAACAATAGTTTATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAA
*
444949 TATATGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTA
66 TATAAGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTA
* * *
445014 TAAACTATGTATACTATATATAAACTATATATATATATATATATATATATA-TATATAACA-TAT
131 TAAACTATGTATAGTATATATAAACTATATATATATACATATATATATAAACTATATAA-AGTA-
* *** * * * *** * **
445077 ACA-TATATATATAAACTATATAAA--GTAAATTACATATATAGTTTATA---GAAACCCTCA-A
194 A-ATTACATATATAGTTTATAGAAACCCTAAA-CAC-TA-A-ACCCTAAACCTGAAATACT-ATA
* * * *
445135 CCCTAAACCCTCAACGATATATA-TATAGACACAATTAATAATTCATATATAGTTT
253 --CTAAA--CACAA--ATATATAGTATAGTCACAATTCATAAGT-ATATATA---T
*
445190 ATATAAACAATAGTTTATATAAATTATATATGTAACATTAACCTATAGTCTATAAATAATAGTTA
1 -TATAAACAATAGTTTATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTA
*
445255 ATATATGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGT
65 ATATAAGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGT
* *
445320 ATAAACTATGTATAGTATATATAAACTATATATATATATATATATATATAAATTATATAAAGTAA
130 ATAAACTATGTATAGTATATATAAACTATATATATATACATATATATATAAACTATATAAAGTAA
* * *
445385 ATTACTTATATAGTTTATAGAAACCCTAAACATTAAACCCTAAACCTTAAATACTATACCCTAAA
195 ATTACATATATAGTTTATAGAAACCCTAAACACTAAACCCTAAACCTGAAATACTATA--CTAAA
* *
445450 CCCTAAATGATATATGTATAGTCACAATTCATAATTCATATATAGTTT
258 CAC-AAAT-ATATA-GTATAGTCACAATTCATAAGT-ATATATA---T
445498 ATATAAACAATAGTTTATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTA
1 -TATAAACAATAGTTTATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTA
*
445563 ATATAAGTAACCTATAGTATATGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGT
65 ATATAAGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGT
* *
445628 CTAAACTATGTATAGTATATATAAACTATATGTATATA
130 ATAAACTATGTATAGTATATATAAACTATATATATATA
445666 ACCTATAGTA
Statistics
Matches: 434, Mismatches: 28, Indels: 25
0.89 0.06 0.05
Matches are distributed among these distances:
305 6 0.01
306 9 0.02
307 199 0.46
308 216 0.50
309 4 0.01
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (298 bp):
TATAAACAATAGTTTATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAA
TATAAGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTA
TAAACTATGTATAGTATATATAAACTATATATATATACATATATATATAAACTATATAAAGTAAA
TTACATATATAGTTTATAGAAACCCTAAACACTAAACCCTAAACCTGAAATACTATACTAAACAC
AAATATATAGTATAGTCACAATTCATAAGTATATATAT
Found at i:445396 original size:2 final size:2
Alignment explanation
Indices: 445330--445378 Score: 55
Period size: 2 Copynumber: 24.0 Consensus size: 2
445320 ATAAACTATG
* *
445330 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA AA T-
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
445373 TA TA TA
1 TA TA TA
445379 AAGTAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 1 0.03
2 36 0.90
3 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:445415 original size:7 final size:7
Alignment explanation
Indices: 445405--445456 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
445395 TAGTTTATAG
445405 AAACCCT
1 AAACCCT
**
445412 AAACATT
1 AAACCCT
445419 AAACCCT
1 AAACCCT
*
445426 AAACCTT
1 AAACCCT
**
445433 AAATACT
1 AAACCCT
*
445440 ATACCCT
1 AAACCCT
445447 AAACCCT
1 AAACCCT
445454 AAA
1 AAA
445457 TGATATATGT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:445463 original size:21 final size:21
Alignment explanation
Indices: 445405--445457 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
445395 TAGTTTATAG
* * *
445405 AAACCCTAAACATTAAACCCT
1 AAACCCTAAATACTATACCCT
*
445426 AAACCTTAAATACTATACCCT
1 AAACCCTAAATACTATACCCT
445447 AAACCCTAAAT
1 AAACCCTAAAT
445458 GATATATGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCCTAAATACTATACCCT
Found at i:445575 original size:308 final size:306
Alignment explanation
Indices: 444838--445665 Score: 1249
Period size: 307 Copynumber: 2.7 Consensus size: 306
444828 CTAAACTTTA
* * * *
444838 TAAACTATATATGTATAGACACAGTTGATAATTCATATATAGTTTATATAAACAATAGTTCATAT
1 TAAACGATATATGTATAGACACAATTAATAATTCATATATAGTTTATATAAACAATAGTTTATAT
444903 AAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATATATGTAACCTATAGTAT
66 AAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATATATGTAACCTATAGTAT
*
444968 ATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATACTATAT
131 ATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATAGTATAT
* *
445033 ATAAACTATATATATATATATATATATATATATATATAACATATACATATATATATAAACTATAT
196 ATAAACTATATATATATATATATATATATAAATATATAACATATACATATATATATAAACTATAG
* * * * **
445098 AAAGTAAATTACATATATAGTTTATAGAAACCCTCAACCCTAAACCC
261 AAACTAAATTAAACATAAACCTTATAGAAA-CCTCAACCCTAAACCC
* *
445145 TCAACGATATATATATAGACACAATTAATAATTCATATATAGTTTATATAAACAATAGTTTATAT
1 TAAACGATATATGTATAGACACAATTAATAATTCATATATAGTTTATATAAACAATAGTTTATAT
*
445210 AAATTATATATGTAACATTAACCTATAGTCTATAAATAATAGTTAATATATGTAACCTATAGTAT
66 AAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATATATGTAACCTATAGTAT
445275 ATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATAGTATAT
131 ATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATAGTATAT
***
445340 ATAAACTATATATATATATATATATATATAAATTATATAA-AGTA-A-AT-TACTTATATAGTTT
196 ATAAACTATATATATATATATATATATATAAA-TATATAACA-TATACATATA--TATATAAACT
* *
445401 ATAGAAACCCTAAACATTAAACCCTAAACCTTA-A-ATA-CT-ATACCCTAAACCC
257 ATAGAAA--CT-AA-ATTAAA-CATAAACCTTATAGAAACCTCA-ACCCTAAACCC
* * *
445453 TAAATGATATATGTATAGTCACAATTCATAATTCATATATAGTTTATATAAACAATAGTTTATAT
1 TAAACGATATATGTATAGACACAATTAATAATTCATATATAGTTTATATAAACAATAGTTTATAT
*
445518 AAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATATAAGTAACCTATAGTAT
66 AAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATATATGTAACCTATAGTAT
* *
445583 ATGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTCTAAACTATGTATAGTATAT
131 ATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATAGTATAT
*
445648 ATAAACTATATGTATATA
196 ATAAACTATATATATATA
445666 ACCTATAGTA
Statistics
Matches: 480, Mismatches: 31, Indels: 19
0.91 0.06 0.04
Matches are distributed among these distances:
305 2 0.00
306 2 0.00
307 234 0.49
308 225 0.47
309 1 0.00
310 4 0.01
311 6 0.01
312 6 0.01
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.38
Consensus pattern (306 bp):
TAAACGATATATGTATAGACACAATTAATAATTCATATATAGTTTATATAAACAATAGTTTATAT
AAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATATATGTAACCTATAGTAT
ATGTATACATATAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATAGTATAT
ATAAACTATATATATATATATATATATATAAATATATAACATATACATATATATATAAACTATAG
AAACTAAATTAAACATAAACCTTATAGAAACCTCAACCCTAAACCC
Found at i:445646 original size:57 final size:58
Alignment explanation
Indices: 445574--445731 Score: 180
Period size: 57 Copynumber: 2.7 Consensus size: 58
445564 TATAAGTAAC
* * * *
445574 CTATAGTATATGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTCTA-AA-
1 CTAT-GTATATGTAT--ATATAAACTATATATGTAACCTATAGTACATGTATATATACAAT
* *
445633 CTATGTATA-GTATATATAAACTATATGTATATAACCTATAGTATATGTATATATACAAT
1 CTATGTATATGTATATATAAACTATA--TATGTAACCTATAGTACATGTATATATACAAT
*
445692 CTATTTATATGT-TATATAAACTATATATGTAACCTATAGT
1 CTATGTATATGTATATATAAACTATATATGTAACCTATAGT
445732 TTATAAACAA
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
55 11 0.13
57 41 0.48
58 7 0.08
59 25 0.29
60 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (58 bp):
CTATGTATATGTATATATAAACTATATATGTAACCTATAGTACATGTATATATACAAT
Found at i:445665 original size:15 final size:14
Alignment explanation
Indices: 445645--445678 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
445635 ATGTATAGTA
445645 TATATAAACTATATG
1 TATATAAACTATA-G
*
445660 TATATAACCTATAG
1 TATATAAACTATAG
445674 TATAT
1 TATAT
445679 GTATATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
TATATAAACTATAG
Found at i:445715 original size:20 final size:21
Alignment explanation
Indices: 445654--445716 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
445644 ATATATAAAC
*
445654 TATATG-TATATAACCTATAG
1 TATATGTTATATAAACTATAG
*
445674 TATATGTATATATACAATCTAT-T
1 TATATGT-TATATA-AA-CTATAG
445697 TATATGTTATATAAACTATA
1 TATATGTTATATAAACTATA
445717 TATGTAACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 10 0.28
21 2 0.06
22 12 0.33
23 8 0.22
24 4 0.11
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (21 bp):
TATATGTTATATAAACTATAG
Found at i:445786 original size:21 final size:21
Alignment explanation
Indices: 445760--445807 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
445750 ATTATTGTAC
* *
445760 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
445781 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
445802 TTTATA
1 TATATA
445808 TTAATGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:445890 original size:36 final size:36
Alignment explanation
Indices: 445847--445925 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
445837 TAATTATCTT
*
445847 AACTATAACTTATATTAATAAAGTATATAGTTTATA
1 AACTATAACTTATATTAATAAAGTAGATAGTTTATA
* * * **
445883 AATTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAACTTATATTAATAAAGTAGATAGTTTATA
445919 AACTATA
1 AACTATA
445926 GTTTACATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (36 bp):
AACTATAACTTATATTAATAAAGTAGATAGTTTATA
Found at i:445936 original size:36 final size:36
Alignment explanation
Indices: 445847--445937 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
445837 TAATTATCTT
* * ** *
445847 AACTATAACTTATATTAATAAAGTATATAGTTTATA
1 AACTATAATTTACATTAATGTAGTAGATAGTTTATA
* **
445883 AATTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTACATTAATGTAGTAGATAGTTTATA
*
445919 AACTATAGTTTACATTAAT
1 AACTATAATTTACATTAAT
445938 ATTAACATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (36 bp):
AACTATAATTTACATTAATGTAGTAGATAGTTTATA
Found at i:446113 original size:32 final size:31
Alignment explanation
Indices: 446013--446126 Score: 77
Period size: 35 Copynumber: 3.5 Consensus size: 31
446003 AACCATATAC
* * * *
446013 TATATTAATATAAATTATATTAACTATAGTT
1 TATATTAATATTAATTTTATAAAATATAGTT
*
446044 TATAAACTATACTATATAA-TTTATAAAATATAGTT
1 TAT--A-T-TAATAT-TAATTTTATAAAATATAGTT
* * * * *
446079 TATCTTTGATATTAATTTTATAGACTATATTT
1 TAT-ATTAATATTAATTTTATAAAATATAGTT
446111 TATATTAATATTAATT
1 TATATTAATATTAATT
446127 ACAAATTATA
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
31 17 0.27
32 20 0.32
33 2 0.03
34 1 0.02
35 21 0.33
36 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (31 bp):
TATATTAATATTAATTTTATAAAATATAGTT
Found at i:446182 original size:15 final size:15
Alignment explanation
Indices: 446162--446223 Score: 83
Period size: 15 Copynumber: 4.2 Consensus size: 15
446152 ATATAAGTCA
*
446162 ATATTATTATTAATT
1 ATATTAATATTAATT
446177 ATATTAATATTAATT
1 ATATTAATATTAATT
*
446192 ATAAT-ATA-TAATGT
1 ATATTAATATTAAT-T
446206 ATATTAATATTAATT
1 ATATTAATATTAATT
446221 ATA
1 ATA
446224 AATAGTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.10
14 8 0.20
15 25 0.61
16 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTAATATTAATT
Found at i:446234 original size:24 final size:28
Alignment explanation
Indices: 446164--446249 Score: 105
Period size: 24 Copynumber: 3.3 Consensus size: 28
446154 ATAAGTCAAT
446164 ATTAT-TAT-TAAT-TATATTAATATTA
1 ATTATATATATAATGTATATTAATATTA
446189 ATTATAATATATAATGTATATTAATATTA
1 ATTAT-ATATATAATGTATATTAATATTA
*
446218 ATTATA-A-AT-A-GTTTATTAATATTA
1 ATTATATATATAATGTATATTAATATTA
446242 ATTATATA
1 ATTATATA
446250 GGGATGAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
24 19 0.35
25 7 0.13
26 2 0.04
27 4 0.07
28 5 0.09
29 18 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTATATATATAATGTATATTAATATTA
Found at i:446234 original size:65 final size:65
Alignment explanation
Indices: 446110--446248 Score: 156
Period size: 65 Copynumber: 2.1 Consensus size: 65
446100 AGACTATATT
* *
446110 TTATATTAATATTAATTACAAATTATAAACTATATAATATTCATATAAGTCAATATTATTATTAA
1 TTATATTAATATTAATTACAAATTATAAACTATATAATATTAATATAAATCAATATTATTATTAA
* ** * *
446175 TTATATTAATATTAATTA-TAATATATAATGTATATTAATATTAATTATAAAT-AGTTTATTAAT
1 TTATATTAATATTAATTACAAAT-TATAAACTATA-TAATATTAA-TATAAATCA--ATATTATT
446238 ATTAA
61 ATTAA
446243 TTATAT
1 TTATAT
446249 AGGGATGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
64 3 0.05
65 27 0.44
66 9 0.15
67 6 0.10
68 17 0.27
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (65 bp):
TTATATTAATATTAATTACAAATTATAAACTATATAATATTAATATAAATCAATATTATTATTAA
Found at i:446496 original size:20 final size:20
Alignment explanation
Indices: 446471--446518 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
446461 CATTTTGCTC
*
446471 TCTCTCTCAAA-CTCTCCGAT
1 TCTCTCTAAAATCTCTCC-AT
446491 TCTCTC-AAAATTCTCTCCAT
1 TCTCTCTAAAA-TCTCTCCAT
446511 TCTCTCTA
1 TCTCTCTA
446519 GAAGTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.21, C:0.38, G:0.02, T:0.40
Consensus pattern (20 bp):
TCTCTCTAAAATCTCTCCAT
Found at i:446963 original size:12 final size:12
Alignment explanation
Indices: 446948--446986 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
446938 TAACCTCAAC
*
446948 CCCAAACTTGAA
1 CCCAAACTCGAA
* *
446960 CCCAAACCCAAA
1 CCCAAACTCGAA
446972 CCCAAACTCGAA
1 CCCAAACTCGAA
446984 CCC
1 CCC
446987 GAACCCACAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.46, G:0.05, T:0.08
Consensus pattern (12 bp):
CCCAAACTCGAA
Found at i:446967 original size:6 final size:6
Alignment explanation
Indices: 446958--447017 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
446948 CCCAAACTTG
* * * * * *
446958 AACCCA AACCCA AACCCA AACTCG AACCCG AACCCA CACTCG AACCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
*
447006 AACCTA AACCCA
1 AACCCA AACCCA
447018 CACCGAACTC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.43, C:0.47, G:0.05, T:0.05
Consensus pattern (6 bp):
AACCCA
Found at i:446971 original size:18 final size:18
Alignment explanation
Indices: 446964--447014 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
446954 CTTGAACCCA
446964 AACCCAAACCCAAACTCG
1 AACCCAAACCCAAACTCG
* *
446982 AACCCGAACCCACACTCG
1 AACCCAAACCCAAACTCG
*
447000 AACCCAAACCTAAAC
1 AACCCAAACCCAAAC
447015 CCACACCGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.45, G:0.06, T:0.06
Consensus pattern (18 bp):
AACCCAAACCCAAACTCG
Found at i:446984 original size:24 final size:24
Alignment explanation
Indices: 446939--446993 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
446929 ACCTAACCTT
* *
446939 AACCTCAACCCCAAACTTGAACCCA
1 AACC-CAAACCCAAACTCGAACCCA
*
446964 AACCCAAACCCAAACTCGAACCCG
1 AACCCAAACCCAAACTCGAACCCA
446988 AACCCA
1 AACCCA
446994 CACTCGAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.42, C:0.45, G:0.05, T:0.07
Consensus pattern (24 bp):
AACCCAAACCCAAACTCGAACCCA
Found at i:449519 original size:23 final size:24
Alignment explanation
Indices: 449491--449544 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
449481 ATATTATTTT
449491 TTTACATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
449514 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
449538 TTTACAT
1 TTTACAT
449545 TTAATCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 20 0.67
24 10 0.33
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:449618 original size:13 final size:13
Alignment explanation
Indices: 449564--449626 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 13
449554 GTTCAATGCC
*
449564 AATAATCTTATT-
1 AATAATTTTATTA
*
449576 AATAATGTT-TTA
1 AATAATTTTATTA
* *
449588 TATAATTTACATTTA
1 AATAATTT-TA-TTA
449603 AATAATTTTATTA
1 AATAATTTTATTA
449616 AATAATTTTAT
1 AATAATTTTAT
449627 ATAATAAGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 2 0.05
12 14 0.34
13 14 0.34
14 1 0.02
15 10 0.24
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (13 bp):
AATAATTTTATTA
Found at i:449632 original size:13 final size:12
Alignment explanation
Indices: 449564--449633 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 12
449554 GTTCAATGCC
*
449564 AATAATCTTATT
1 AATAATTTTATT
*
449576 AATAATGTT-TT
1 AATAATTTTATT
*
449587 ATATAATTTACATTT
1 A-ATAATTT-TA-TT
449602 AAATAATTTTATT
1 -AATAATTTTATT
449615 AAATAATTTTATAT
1 -AATAATTTTAT-T
449629 AATAA
1 AATAA
449634 GTCTATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
11 3 0.06
12 14 0.29
13 19 0.40
14 2 0.04
15 9 0.19
16 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (12 bp):
AATAATTTTATT
Found at i:449865 original size:16 final size:16
Alignment explanation
Indices: 449844--449907 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
449834 TTTACAAGTA
449844 AGGTTAAAAACAGGTC
1 AGGTTAAAAACAGGTC
449860 AGGTTAAAAACAGGTC
1 AGGTTAAAAACAGGTC
* ** *
449876 AGGTTCATCATAGGTC
1 AGGTTAAAAACAGGTC
*
449892 AGGTTGAAAACAGGTC
1 AGGTTAAAAACAGGTC
449908 GGGTAATACC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.22
Consensus pattern (16 bp):
AGGTTAAAAACAGGTC
Found at i:450165 original size:26 final size:26
Alignment explanation
Indices: 450129--450188 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
450119 ATGTTAAAAA
*
450129 CAGTTTTAACTCGAGTCGGTTTCAGT
1 CAGTTTTAACTCGAGTCAGTTTCAGT
*
450155 CAGTTTTAACTCTAGTCAGTTTCAGT
1 CAGTTTTAACTCGAGTCAGTTTCAGT
*
450181 CACTTTTA
1 CAGTTTTA
450189 CAGATCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (26 bp):
CAGTTTTAACTCGAGTCAGTTTCAGT
Found at i:450446 original size:21 final size:21
Alignment explanation
Indices: 450420--450463 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
450410 GTTTCCAGAT
450420 TCGCAACGAGAACATCGACTA
1 TCGCAACGAGAACATCGACTA
* *
450441 TCGCAACGCGAACTTCGACTA
1 TCGCAACGAGAACATCGACTA
450462 TC
1 TC
450464 ACAATGCGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (21 bp):
TCGCAACGAGAACATCGACTA
Found at i:450472 original size:21 final size:21
Alignment explanation
Indices: 450423--450472 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
450413 TCCAGATTCG
* *
450423 CAACGAGAACATCGACTATCG
1 CAACGCGAACATCGACTATCA
*
450444 CAACGCGAACTTCGACTATCA
1 CAACGCGAACATCGACTATCA
*
450465 CAATGCGA
1 CAACGCGA
450473 TTTTCCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.16
Consensus pattern (21 bp):
CAACGCGAACATCGACTATCA
Found at i:450514 original size:21 final size:21
Alignment explanation
Indices: 450484--450698 Score: 212
Period size: 21 Copynumber: 10.4 Consensus size: 21
450474 TTTCCAAATT
* *
450484 CGTTGTGATAATCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
450505 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
450526 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
450547 TGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
450566 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
450587 CATTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
450608 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
450627 TGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
450648 CGTTGCGATTTATTCCAA--ACT
1 CGTTGCGA--TAGTCCAAGTTCG
*
450669 CGTTGTGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
450690 CATTGCGAT
1 CGTTGCGAT
450699 TTATTCCAAA
Statistics
Matches: 159, Mismatches: 25, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
19 50 0.31
21 95 0.60
23 14 0.09
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:450541 original size:61 final size:60
Alignment explanation
Indices: 450468--450698 Score: 295
Period size: 61 Copynumber: 3.8 Consensus size: 60
450458 ACTATCACAA
* * *
450468 TGCGATT-TTCCAAATTCGTTGTGATAATCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTATTCCAAATTCGTTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGT
* * *
450529 TGCGA-TAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCAT
1 TGCGATTATTCCAAATTC--GTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
450590 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTTGTTGCGATAGTCGAAGTTCGCGT
1 TGCGA-TTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
450651 TGCGATTTATTCCAAACTCGTTGTGATAGTCCAAGTTCGCATTGCGAT
1 TGCGA-TTATTCCAAATTCGTTGCGATAGTCCAAGTTCG--TTGCGAT
450699 TTATTCCAAA
Statistics
Matches: 150, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
60 1 0.01
61 116 0.77
63 33 0.22
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (60 bp):
TGCGATTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:450687 original size:103 final size:102
Alignment explanation
Indices: 450505--450726 Score: 329
Period size: 103 Copynumber: 2.2 Consensus size: 102
450495 TCCAAGTTCG
* **
450505 CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGTGTTGCGATAGTCCAAGTTCGTT
1 CGTTGCGATAGTCCAAGTTC-CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAACTCGTT
*
450570 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATT
65 GCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
* * *
450608 CGTTGCGATAGTCCAAGTT-TGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAACTCGT
1 CGTTGCGATAGTCCAAGTTCCGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAACTCGT
*
450672 TGTGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
64 TGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
*
450711 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
450727 AATCGCAACG
Statistics
Matches: 108, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
101 26 0.24
103 82 0.76
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (102 bp):
CGTTGCGATAGTCCAAGTTCCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAACTCGTTG
CGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATT
Found at i:450699 original size:42 final size:42
Alignment explanation
Indices: 450628--450726 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
450618 GTCCAAGTTT
* * *
450628 GTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAACTC
1 GTTGTGATAGTCCAAGTTCGCATTGCGATTTATTCCAAACTC
*
450670 GTTGTGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTC
1 GTTGTGATAGTCCAAGTTCGCATTGCGATTTATTCCAAACTC
450712 GTTGTGATAGTCCAA
1 GTTGTGATAGTCCAA
450727 AATCGCAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (42 bp):
GTTGTGATAGTCCAAGTTCGCATTGCGATTTATTCCAAACTC
Found at i:451465 original size:6 final size:6
Alignment explanation
Indices: 451454--451480 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
451444 TCTCGTCTCG
451454 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
451481 AATGCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:451524 original size:21 final size:21
Alignment explanation
Indices: 451499--451568 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
451489 TTTCCAAATT
451499 CGTTGCGATAGTCCAAGTTTG
1 CGTTGCGATAGTCCAAGTTTG
*
451520 CGTTGTGATAGTCCAAG-TT-
1 CGTTGCGATAGTCCAAGTTTG
* *
451539 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTTG
451560 CGTTGCGAT
1 CGTTGCGAT
451569 TTCTTCCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.35
20 3 0.07
21 25 0.58
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTTG
Found at i:451591 original size:42 final size:42
Alignment explanation
Indices: 451490--451638 Score: 203
Period size: 42 Copynumber: 3.6 Consensus size: 42
451480 TAATGCAATT
* *
451490 TTCCAAATTCGTTGCGATAGTCCAAGTTTGCGTTGTGA--TA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
* * * *
451530 GTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTC
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
* *
451572 TTCCAAATTCGTTGTGATAGTCCAAGTTCGCATTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
*
451614 TTCCAAATTCGTTGCGATAATCCAA
1 TTCCAAATTCGTTGCGATAGTCCAA
451639 AATCGCAACG
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 33 0.35
42 60 0.65
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
Found at i:451624 original size:23 final size:21
Alignment explanation
Indices: 451560--451631 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
451550 TCGAAGTTCG
*
451560 CGTTGCGATTTCTTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
451581 CGTTGTGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
451600 CGCATTGCGATTTATTCCAAATT
1 CG--TTGCGATTTATTCCAAATT
451623 CGTTGCGAT
1 CGTTGCGAT
451632 AATCCAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
19 10 0.25
21 19 0.47
23 11 0.28
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:451638 original size:61 final size:58
Alignment explanation
Indices: 451490--451639 Score: 149
Period size: 61 Copynumber: 2.4 Consensus size: 58
451480 TAATGCAATT
* *
451490 TTCCAAATTCGTTGCGATAGTCCAAGTTTGCGTTGTGATAGTCCAAGTTCGTTGCGATA
1 TTCCAAATTCGTTGCGATAATCCAA-ATTGCGTTGTGATAGTCCAAGTTCGTTGCGATA
* * * **
451549 GTCGAAGTTCGCGTTGCGATTTCTTCCAAATT-CGTTGTGATAGTCCAAGTTCGCATTGCGATTT
1 TTCCAAATT--CGTTGCGA--TAATCCAAATTGCGTTGTGATAGTCCAAGTTCG--TTGCGA--T
451613 A
58 A
451614 TTCCAAATTCGTTGCGATAATCCAAA
1 TTCCAAATTCGTTGCGATAATCCAAA
451640 ATCGCAACGA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
59 6 0.08
61 36 0.50
62 2 0.03
63 20 0.28
65 8 0.11
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (58 bp):
TTCCAAATTCGTTGCGATAATCCAAATTGCGTTGTGATAGTCCAAGTTCGTTGCGATA
Found at i:451739 original size:6 final size:6
Alignment explanation
Indices: 451728--451754 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
451718 GACACGTATT
451728 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
451755 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:451901 original size:38 final size:39
Alignment explanation
Indices: 451854--451931 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
451844 CCTTAAATAC
* *
451854 CATTCCCAACA-GTGTTTCCAATACTATGTGGGATTGAG
1 CATTACCAACACGTGTTCCCAATACTATGTGGGATTGAG
*
451892 CATTACCAACACTTGTTCCCAATACTATGTGGGATTGAG
1 CATTACCAACACGTGTTCCCAATACTATGTGGGATTGAG
451931 C
1 C
451932 CTTAAATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 10 0.28
39 26 0.72
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (39 bp):
CATTACCAACACGTGTTCCCAATACTATGTGGGATTGAG
Found at i:452539 original size:21 final size:19
Alignment explanation
Indices: 452506--452703 Score: 144
Period size: 19 Copynumber: 9.7 Consensus size: 19
452496 CGTTGCAATT
* *
452506 TTGGATTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
452525 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * *
452548 TTGGACTATCACAACGAAT
1 TTGGAATATCGCAACGAAC
*
452567 TTGGAAGAAATCGCAACGCAAAC
1 TTGG-A-ATATCGCAACG--AAC
* *
452590 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
* *
452609 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
452628 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
452651 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
*
452670 TTGGACTATCGCAACGCAAAC
1 TTGGAATATCGCAACG--AAC
*
452691 TTGGACTATCGCA
1 TTGGAATATCGCA
452704 TTGCGATAGT
Statistics
Matches: 146, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
19 60 0.41
20 1 0.01
21 60 0.41
22 1 0.01
23 24 0.16
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:452565 original size:42 final size:42
Alignment explanation
Indices: 452506--452613 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
452496 CGTTGCAATT
* * *
452506 TTGGATTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAAGAAATCGCAACGCAAAC
*
452548 TTGGACTATCACAACGAATTTGGAAGAAATCGCAACGCAAAC
1 TTGGACTATCGCAACGAATTTGGAAGAAATCGCAACGCAAAC
* *
452590 TTCGACTATCGCAACGAACTTGGA
1 TTGGACTATCGCAACGAATTTGGA
452614 CTATCGCAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAAGAAATCGCAACGCAAAC
Found at i:452615 original size:61 final size:61
Alignment explanation
Indices: 452534--452685 Score: 259
Period size: 61 Copynumber: 2.5 Consensus size: 61
452524 TTTGGAATAA
*
452534 ATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAAGAAATCGCAACGCAAACTTCGACT
1 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAAGAAATCGCAACGCAAACTTCGACT
* *
452597 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAAGAAATCGCAACGCAAACTTCGACT
452658 ATCGCAACGAACTTGGACTATCGCAACG
1 ATCGCAACGAACTTGGACTATCGCAACG
452686 CAAACTTGGA
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
61 79 0.92
63 7 0.08
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (61 bp):
ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAAGAAATCGCAACGCAAACTTCGACT
Found at i:452641 original size:40 final size:38
Alignment explanation
Indices: 452506--452703 Score: 153
Period size: 42 Copynumber: 4.8 Consensus size: 38
452496 CGTTGCAATT
* * *
452506 TTGGATTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAACTTGGACT--ATCGCAA--CGAAC
* * * **
452548 TTGGACTATCACAACGAATTTGGAAGAAATCGCAACGCAAAC
1 TTGGAATATCGCAACGAACTTGG-A-CTATCGCAACG--AAC
* * *
452590 TTCGACTATCGCAACGAACTTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAACTTGGACTATCGCAACGAAC
*
452628 TTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGAAT--ATCGCAA--CGAACTTGGACTATCGCAACGAAC
*
452670 TTGGACTATCGCAACGCAAACTTGGACTATCGCA
1 TTGGAATATCGCAACG--AACTTGGACTATCGCA
452704 TTGCGATAGT
Statistics
Matches: 131, Mismatches: 15, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
38 9 0.07
40 40 0.31
41 1 0.01
42 79 0.60
43 1 0.01
44 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (38 bp):
TTGGAATATCGCAACGAACTTGGACTATCGCAACGAAC
Found at i:452702 original size:61 final size:60
Alignment explanation
Indices: 452534--452703 Score: 225
Period size: 61 Copynumber: 2.8 Consensus size: 60
452524 TTTGGAATAA
* * *
452534 ATCGCAACGCGAACTTGGACTATCACAACGAATTTGGAAGAAATCGCAACGCAAACTTCGACT
1 ATCGCAA--CGAACTTGGACTATCGCAACGAACTTGGAA-TAATCGCAACGCAAACTTCGACT
* *
452597 ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCAAACTTCGACT
*
452658 ATCGCAACGAACTTGGACTATCGCAACGCAAACTTGGACT-ATCGCA
1 ATCGCAACGAACTTGGACTATCGCAACG--AACTTGGAATAATCGCA
452704 TTGCGATAGT
Statistics
Matches: 99, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
61 84 0.85
63 15 0.15
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
ATCGCAACGAACTTGGACTATCGCAACGAACTTGGAATAATCGCAACGCAAACTTCGACT
Found at i:452723 original size:21 final size:21
Alignment explanation
Indices: 452699--452751 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
452689 ACTTGGACTA
*
452699 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
452720 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
452741 TCGCGTTGCGA
1 TCGCGTTGCGA
452752 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:453293 original size:36 final size:36
Alignment explanation
Indices: 453244--453328 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
453234 TAAAAAATTT
* * *
453244 AAAAATATGAAATTAAATAATTAATAGAAAATATAA
1 AAAAATCTAAAATTAAATAATTAATAAAAAATATAA
453280 AAAAATCTAAAATTAAATAATTAATAAAAAATATAA
1 AAAAATCTAAAATTAAATAATTAATAAAAAATATAA
453316 AAAAATCTAAAAT
1 AAAAATCTAAAAT
453329 ATTTCTTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (36 bp):
AAAAATCTAAAATTAAATAATTAATAAAAAATATAA
Found at i:453327 original size:17 final size:17
Alignment explanation
Indices: 453271--453330 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
453261 TAATTAATAG
453271 AAAATATAAAAAAATCT
1 AAAATATAAAAAAATCT
**
453288 AAAAT-TAAATAATTAATAA
1 AAAATATAAA-AA--AATCT
453307 AAAATATAAAAAAATCT
1 AAAATATAAAAAAATCT
453324 AAAATAT
1 AAAATAT
453331 TTCTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 17 0.49
19 10 0.29
20 4 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATATAAAAAAATCT
Found at i:453550 original size:87 final size:87
Alignment explanation
Indices: 453404--453578 Score: 305
Period size: 87 Copynumber: 2.0 Consensus size: 87
453394 AGTGAGGGCC
453404 GCTGGTGTCTAGTCAAGAAAAAGAAAAGAAGGCTACTGGTGAGATTAGTATTATTATGGCGGCGA
1 GCTGGTGTCTAGTCAAGAAAAAGAAAAGAAGGCTACTGGTGAGATTAGTATTATTATGGCGGCGA
453469 GTAACGGTCCATGCAGGAGGCT
66 GTAACGGTCCATGCAGGAGGCT
* * *
453491 GCTGGTGTCTATTGAAGAAAAAGAAAAGAAGGCTGCTGGTGAGATTAGTATTATTATGGCGGCGA
1 GCTGGTGTCTAGTCAAGAAAAAGAAAAGAAGGCTACTGGTGAGATTAGTATTATTATGGCGGCGA
* *
453556 GTGACGGTCCATTCAGGAGGCT
66 GTAACGGTCCATGCAGGAGGCT
453578 G
1 G
453579 AAAAAGAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (87 bp):
GCTGGTGTCTAGTCAAGAAAAAGAAAAGAAGGCTACTGGTGAGATTAGTATTATTATGGCGGCGA
GTAACGGTCCATGCAGGAGGCT
Found at i:454027 original size:11 final size:10
Alignment explanation
Indices: 454005--454063 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
453995 TTCACTTTTT
*
454005 TAAAAATAAA
1 TAAAAATGAA
454015 TAAAAATGCAA
1 TAAAAATG-AA
*
454026 TAAAAAAGAA
1 TAAAAATGAA
454036 TTAAAAATGAA
1 -TAAAAATGAA
* *
454047 TAAAATTTAA
1 TAAAAATGAA
454057 TAAAAAT
1 TAAAAAT
454064 ATCACCTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (10 bp):
TAAAAATGAA
Found at i:454031 original size:21 final size:20
Alignment explanation
Indices: 454005--454063 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
453995 TTCACTTTTT
454005 TAAAAATAAATAAAAATGCAA
1 TAAAAATAAATAAAAATG-AA
454026 TAAAAA-AGAATTAAAAATGAA
1 TAAAAATA-AA-TAAAAATGAA
* *
454047 TAAAATTTAATAAAAAT
1 TAAAAATAAATAAAAAT
454064 ATCACCTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 8 0.24
21 17 0.52
22 8 0.24
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
TAAAAATAAATAAAAATGAA
Found at i:454151 original size:29 final size:31
Alignment explanation
Indices: 454113--454186 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
454103 TTAAAAATAT
454113 AAAATAAATATTAA-ATT-TTAATT-TTATTA
1 AAAAT-AATATTAATATTATTAATTGTTATTA
*
454142 AAAATGAATA--AATATTATTAATTGTTGTTA
1 AAAAT-AATATTAATATTATTAATTGTTATTA
454172 AAAATAATAATTAAT
1 AAAATAAT-ATTAAT
454187 GAATAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 2 0.05
28 3 0.08
29 18 0.49
30 11 0.30
32 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (31 bp):
AAAATAATATTAATATTATTAATTGTTATTA
Found at i:455086 original size:11 final size:10
Alignment explanation
Indices: 455040--455098 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
455030 CTTTACATTA
455040 TATTTTTATT
1 TATTTTTATT
* *
455050 GAATTTTATT
1 TATTTTTATT
* * *
455060 CATGTTTAAT
1 TATTTTTATT
455070 TATTTTTATT
1 TATTTTTATT
455080 GTATTTTTATT
1 -TATTTTTATT
455091 TATTTTTA
1 TATTTTTA
455099 AAAAAATGAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 29 0.74
11 10 0.26
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (10 bp):
TATTTTTATT
Found at i:458100 original size:222 final size:222
Alignment explanation
Indices: 457713--458868 Score: 1708
Period size: 222 Copynumber: 5.2 Consensus size: 222
457703 AACGGAAATG
** * * * * * * *
457713 TTGAAAACATTC-TGCCCAAAGGTTTTATGAATGACCCGAAGGACTTATCCTCTTGCTCGAAAGG
1 TTGAAAACA-TCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGG
* * * *
457777 CTTACAGATGACCCGAAGGTTTTAAGCATCATGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGT
65 CTTACAGATGACCCGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGT
* * * * * *
457842 TTTCAAGAAACCCCTTAAAAGGCTTGGTTTCCTCTAACAACTCTATTGAGATAATTAAGAAACCC
130 TGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCC
* *
457907 CTCAAAGGCTTAGTTTCCAATATCTCAT
195 CTGAAAGGCTTAGTTTCCAAAATCTCAT
* * * * * * * *
457935 TTGAAAAAATCCTACCCGGAGGTCTTATGGATGGCCTGTAGGTCTTATCATCTTGCTCGAAAGGC
1 TTGAAAACATCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGGC
*
458000 TTACAGATGACCTGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTT
66 TTACAGATGACCCGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTT
* * * * * *
458065 GTCAAGGAACCCCTTAAAAGGCTTAGCTCCCTCTAACAACTCTATTGAAATAATTAATAAACCCT
131 GTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCC
458130 TGAAAGGCTTAGTTTCCAAAATCTCAT
196 TGAAAGGCTTAGTTTCCAAAATCTCAT
*
458157 TTGAAAACATCATGCCTGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGG-
1 TTGAAAACATCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGGC
*
458221 TTATAGATGACCCAGG-GGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGT
66 TTACAGATGACCC-GGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGT
* *
458285 TGTCAAGGAACCCCTTAAAAGGTTTAGCTTCTTTTAACAACTCTTTTGAGATAATTAAGAAACCC
130 TGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCC
*
458350 CTGAAAGGCTTAGTTTCCAAAATCTCTT
195 CTGAAAGGCTTAGTTTCCAAAATCTCAT
* * * *
458378 TTGAAAACATCATGCCCAGAGGTCTTATGGATGGCCCGGGGGTCTTATCACCTTGCTTGGAAGGC
1 TTGAAAACATCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGGC
*
458443 TTACAGATGACCCGGAGGATTTAAAAATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTT
66 TTACAGATGACCCGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTT
*
458508 GTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTTAA-ACCTCTTTTGAGATAATTAAGAAACCC
131 GTCAAGGAACCCCTTAAAAGGCTTAGCTTCC-TTTAACAACTCTTTTGAGATAATTAAGAAACCC
458572 CTGAAAGGCTTAGTTTCCAAAATCTCAT
195 CTGAAAGGCTTAGTTTCCAAAATCTCAT
* * * ** *
458600 TTGAAAAAATCCTGCCTGGAGGTCTTATGGATGATACGTAGGTCTTATCATCTTGCTTGGAAGGC
1 TTGAAAACATCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGGC
* * * * *
458665 TTATAGATGACCCGAATGATTTAAACATCAAGAAACCCTTAAAAATCAAGCTTACTTTCTTGGTT
66 TTACAGATGACCCGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTT
458730 GTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCC
131 GTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCC
458795 TGAAAGGCTTAGTTTCCAAAATCTCAT
196 TGAAAGGCTTAGTTTCCAAAATCTCAT
* **
458822 TTGAAAACATCTTTTCCGGAGGTCTTATGGATGACCCGGAGGTCTTA
1 TTGAAAACATCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTA
458869 CAAATTCGGA
Statistics
Matches: 846, Mismatches: 82, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
221 211 0.25
222 630 0.74
223 5 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (222 bp):
TTGAAAACATCATGCCCGGAGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGGC
TTACAGATGACCCGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTT
GTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCC
TGAAAGGCTTAGTTTCCAAAATCTCAT
Found at i:458618 original size:443 final size:444
Alignment explanation
Indices: 457732--458868 Score: 1749
Period size: 443 Copynumber: 2.6 Consensus size: 444
457722 TTCTGCCCAA
* * * * * * * *
457732 AGGTTTTATGAATGACCCGAAGGACTTATCCTCTTGCTCGAAAGGCTTACAGATGACCCGAAGGT
1 AGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGGAAGGCTTATAGATGACCCGAAGGA
* * * *
457797 TTTAAGCATCATGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTTTCAAGAAACCCCTTAAAA
66 TTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAA
* * * * *
457862 GGCTTGGTTTCCTCTAACAACTCTATTGAGATAATTAAGAAACCCCTCAAAGGCTTAGTTTCCAA
131 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCAA
* * * * * *
457927 TATCTCATTTGAAAAAATCCTACCCGGAGGTCTTATGGATGGCCTGTAGGTCTTATCATCTTGCT
196 AATCTCATTTGAAAACATCATACCCGGAGGTCTTATGGATGGCCCGGAGGTCTTATCACCTTGCT
* *
457992 CGAAAGGCTTACAGATGACCTGGAGGATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTT
261 CGAAAGGCTTACAGATGACCCGGAGGATTTAAAAATCAAGAAACCCTTGAAAATCAAGCTTAGTT
458057 TCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTCCCTCTAACAACTCTATTGAAATAATTAA
326 TCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTCCCTCTAACAACTCTATTGAAATAATTAA
* * *
458122 TAAACCCTTGAAAGGCTTAGTTTCCAAAATCTCATTTGAAAACATCATGCCTGG
391 GAAACCCCTGAAAGGCTTAGTTTCCAAAATCTCATTTGAAAAAATCATGCCTGG
* *
458176 AGGTCTTATGGATGACCCGGAGGTCTTATCATCTTGCTTGGAAGG-TTATAGATGACCC-AGGGG
1 AGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGGAAGGCTTATAGATGACCCGA-AGG
458239 ATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAA
65 ATTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAA
* *
458304 AGGTTTAGCTTCTTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCA
130 AGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCA
* * * *
458369 AAATCTCTTTTGAAAACATCATGCCCAGAGGTCTTATGGATGGCCCGGGGGTCTTATCACCTTGC
195 AAATCTCATTTGAAAACATCATACCCGGAGGTCTTATGGATGGCCCGGAGGTCTTATCACCTTGC
* *
458434 TTGGAAGGCTTACAGATGACCCGGAGGATTTAAAAATCAAGAAACCCTTGAAAATCAAGCTTAGT
260 TCGAAAGGCTTACAGATGACCCGGAGGATTTAAAAATCAAGAAACCCTTGAAAATCAAGCTTAGT
* * * * *
458499 TTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTTCCTTTTAA-ACCTCTTTTGAGATAATT
325 TTCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGC-TCCCTCTAACAACTCTATTGAAATAATT
*
458563 AAGAAACCCCTGAAAGGCTTAGTTTCCAAAATCTCATTTGAAAAAATCCTGCCTGG
389 AAGAAACCCCTGAAAGGCTTAGTTTCCAAAATCTCATTTGAAAAAATCATGCCTGG
** * *
458619 AGGTCTTATGGATGATACGTAGGTCTTATCATCTTGCTTGGAAGGCTTATAGATGACCCGAATGA
1 AGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGGAAGGCTTATAGATGACCCGAAGGA
* *
458684 TTTAAACATCAAGAAACCCTTAAAAATCAAGCTTACTTTCTTGGTTGTCAAGGAACCCCTTAAAA
66 TTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAA
458749 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCAA
131 GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCAA
* ** *
458814 AATCTCATTTGAAAACATCTTTTCCGGAGGTCTTATGGATGACCCGGAGGTCTTA
196 AATCTCATTTGAAAACATCATACCCGGAGGTCTTATGGATGGCCCGGAGGTCTTA
458869 CAAATTCGGA
Statistics
Matches: 629, Mismatches: 60, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
442 1 0.00
443 393 0.62
444 234 0.37
445 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (444 bp):
AGGTCTTATGGATGACCCGAAGGTCTTATCATCTTGCTTGGAAGGCTTATAGATGACCCGAAGGA
TTTAAACATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTGGTTGTCAAGGAACCCCTTAAAA
GGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAAGAAACCCCTGAAAGGCTTAGTTTCCAA
AATCTCATTTGAAAACATCATACCCGGAGGTCTTATGGATGGCCCGGAGGTCTTATCACCTTGCT
CGAAAGGCTTACAGATGACCCGGAGGATTTAAAAATCAAGAAACCCTTGAAAATCAAGCTTAGTT
TCTTGGTTGTCAAGGAACCCCTTAAAAGGCTTAGCTCCCTCTAACAACTCTATTGAAATAATTAA
GAAACCCCTGAAAGGCTTAGTTTCCAAAATCTCATTTGAAAAAATCATGCCTGG
Found at i:461596 original size:27 final size:27
Alignment explanation
Indices: 461550--461610 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
461540 ATCCTTCAAT
461550 TAAATAAATAAATAAGTTCAAAATAAA
1 TAAATAAATAAATAAGTTCAAAATAAA
*
461577 TAAATAAATATATATA-TTCAAAATAAA
1 TAAATAAATAAATA-AGTTCAAAATAAA
461604 TAAATAA
1 TAAATAA
461611 TCCATAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (27 bp):
TAAATAAATAAATAAGTTCAAAATAAA
Found at i:463922 original size:18 final size:18
Alignment explanation
Indices: 463899--463934 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
463889 ACAACTGTAT
*
463899 TAATACTTCTCATTAATA
1 TAATACTGCTCATTAATA
463917 TAATACTGCTCATTAATA
1 TAATACTGCTCATTAATA
463935 GTCAGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATACTGCTCATTAATA
Found at i:464003 original size:18 final size:18
Alignment explanation
Indices: 463980--464015 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
463970 ACAACTGTAT
*
463980 TAATACTTCTCATTAATA
1 TAATACTGCTCATTAATA
463998 TAATACTGCTCATTAATA
1 TAATACTGCTCATTAATA
464016 GTCAGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATACTGCTCATTAATA
Found at i:464012 original size:81 final size:81
Alignment explanation
Indices: 463877--464085 Score: 400
Period size: 81 Copynumber: 2.6 Consensus size: 81
463867 TTTTTAATAG
*
463877 ATTTGGTATAATACAACTGTATTAATACTTCTCATTAATATAATACTGCTCATTAATAGTCAGTG
1 ATTTGGTGTAATACAACTGTATTAATACTTCTCATTAATATAATACTGCTCATTAATAGTCAGTG
463942 GGGAACCACGCCATTA
66 GGGAACCACGCCATTA
463958 ATTTGGTGTAATACAACTGTATTAATACTTCTCATTAATATAATACTGCTCATTAATAGTCAGTG
1 ATTTGGTGTAATACAACTGTATTAATACTTCTCATTAATATAATACTGCTCATTAATAGTCAGTG
464023 GGGAACCACGCCATTA
66 GGGAACCACGCCATTA
*
464039 ATTTGGTGTAATACAACTGTATTAATACTACTCATTAATATAATACT
1 ATTTGGTGTAATACAACTGTATTAATACTTCTCATTAATATAATACT
464086 ACTTAACAAA
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 126 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (81 bp):
ATTTGGTGTAATACAACTGTATTAATACTTCTCATTAATATAATACTGCTCATTAATAGTCAGTG
GGGAACCACGCCATTA
Found at i:465667 original size:130 final size:130
Alignment explanation
Indices: 465526--465773 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
465516 TATTTATATA
*
465526 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * *
465591 TTAGCACATGATCATGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
465656 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
465721 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
465774 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:465804 original size:130 final size:129
Alignment explanation
Indices: 465540--465804 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
465530 ATTTGGTCCT
* *
465540 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
465605 TGACACGTGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
465670 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
465735 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
465799 -A
128 CA
465800 AAATT
1 AAATT
465805 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Done.