Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007772.1 Hibiscus syriacus cultivar Beakdansim tig00110053_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: 1636317
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:389244 original size:29 final size:29
Alignment explanation
Indices: 389172--389312 Score: 162
Period size: 29 Copynumber: 4.8 Consensus size: 29
389162 ATTTATGTAA
*
389172 TAAGTTAAGATAA-AAT-AAATATATGTTT
1 TAAGTTAAAATAAGAATAAAATATAT-TTT
*
389200 TAAGTTAAGACA-AAGACTAAAATATATTTT
1 TAAGTTAA-A-ATAAGAATAAAATATATTTT
389230 TAAGTTAAAATAAGAATAAAATATATTTT
1 TAAGTTAAAATAAGAATAAAATATATTTT
* * *
389259 TAGGTTAAGATAAGAATAAAATATATTTAA
1 TAAGTTAAAATAAGAATAAAATATATTT-T
* *
389289 TAAGTTAATATAAAAATAAAATAT
1 TAAGTTAAAATAAGAATAAAATAT
389313 TTTAAATGTT
Statistics
Matches: 98, Mismatches: 9, Indels: 10
0.84 0.08 0.09
Matches are distributed among these distances:
28 9 0.09
29 46 0.47
30 35 0.36
31 8 0.08
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.35
Consensus pattern (29 bp):
TAAGTTAAAATAAGAATAAAATATATTTT
Found at i:389284 original size:58 final size:60
Alignment explanation
Indices: 389169--389312 Score: 188
Period size: 59 Copynumber: 2.4 Consensus size: 60
389159 TTAATTTATG
* *
389169 TAATAAGTTAAGATAAAAT-AAATATATGTTTTAAGTTAAGACAAAGACTAAAATATATT
1 TAATAAGTTAAAATAAAATAAAATATATGTTTTAAGTTAAGACAAAGAATAAAATATATT
* * *
389228 T-TTAAGTTAAAATAAGAATAAAATATAT-TTTTAGGTTAAGA-TAAGAATAAAATATATT
1 TAATAAGTTAAAATAA-AATAAAATATATGTTTTAAGTTAAGACAAAGAATAAAATATATT
*
389286 TAATAAGTTAATATAAAAATAAAATAT
1 TAATAAGTTAAAAT-AAAATAAAATAT
389313 TTTAAATGTT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 28 0.38
59 36 0.49
60 10 0.14
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.35
Consensus pattern (60 bp):
TAATAAGTTAAAATAAAATAAAATATATGTTTTAAGTTAAGACAAAGAATAAAATATATT
Found at i:393181 original size:19 final size:21
Alignment explanation
Indices: 393138--393181 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
393128 CAAATTATTT
*
393138 TATTAAAAAATCTTGAAATAC
1 TATTAAAAAATCTTAAAATAC
*
393159 TATTAAAATAT-TTAAAATA-
1 TATTAAAAAATCTTAAAATAC
393178 TATT
1 TATT
393182 TTTAATAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 10 0.48
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
TATTAAAAAATCTTAAAATAC
Found at i:393514 original size:16 final size:17
Alignment explanation
Indices: 393495--393535 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
393485 TTTTTTAAAA
*
393495 TATTATATAAT-TTATT
1 TATTATAAAATGTTATT
393511 TATTATTAAAATGTTATT
1 TATTA-TAAAATGTTATT
393529 T-TTATAA
1 TATTATAA
393536 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTATAAAATGTTATT
Found at i:393585 original size:33 final size:32
Alignment explanation
Indices: 393525--393588 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
393515 ATTAAAATGT
393525 TATTTTTATAATTTTATTAATAAAAATATTAA
1 TATTTTTATAATTTTATTAATAAAAATATTAA
393557 TATTTTTAT-ATTTTATTGAAATAAAAATATTA
1 TATTTTTATAATTTTATT--AATAAAAATATTA
393589 TAAATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 8 0.27
32 9 0.30
33 13 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (32 bp):
TATTTTTATAATTTTATTAATAAAAATATTAA
Found at i:393597 original size:31 final size:31
Alignment explanation
Indices: 393491--393599 Score: 83
Period size: 31 Copynumber: 3.7 Consensus size: 31
393481 TTATTTTTTT
*
393491 AAAATATT-ATATAATT-TA-TTTATT-ATT
1 AAAATATTAATATAATTATATTTTATTAATA
* *
393518 AAAATGTT-AT-T-TTTATAATTTTATTAATA
1 AAAATATTAATATAATTAT-ATTTTATTAATA
**
393547 AAAATATTAATATTTTTATATTTTATTGAAATA
1 AAAATATTAATATAATTATATTTTATT--AATA
393580 AAAATATT-ATA-AATTATATT
1 AAAATATTAATATAATTATATT
393600 AATTATTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
25 2 0.03
26 2 0.03
27 10 0.15
28 6 0.09
29 9 0.13
30 2 0.03
31 16 0.24
32 8 0.12
33 12 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (31 bp):
AAAATATTAATATAATTATATTTTATTAATA
Found at i:393606 original size:33 final size:33
Alignment explanation
Indices: 393530--393599 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
393520 AATGTTATTT
**
393530 TTATAATTTTATT--AATAAAAATATTAATATTT
1 TTAT-ATTTTATTGAAATAAAAATATTAATATAA
393562 TTATATTTTATTGAAATAAAAATATT-ATA-AA
1 TTATATTTTATTGAAATAAAAATATTAATATAA
393593 TTATATT
1 TTATATT
393600 AATTATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 15 0.44
32 7 0.21
33 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (33 bp):
TTATATTTTATTGAAATAAAAATATTAATATAA
Found at i:393658 original size:23 final size:23
Alignment explanation
Indices: 393629--393673 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
393619 AGTGTTATAT
393629 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
393652 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
393674 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:393679 original size:23 final size:23
Alignment explanation
Indices: 393630--393680 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
393620 GTGTTATATT
**
393630 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
393653 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
393676 ATATT
1 ATATT
393681 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:395629 original size:51 final size:51
Alignment explanation
Indices: 395416--395628 Score: 302
Period size: 51 Copynumber: 4.2 Consensus size: 51
395406 TTCGATTATA
* *
395416 GGTGTAAGTGAATAAAATAAACAAGTGTATCACTTAACACATACTTACACC
1 GGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTACACC
* * *
395467 GGTGTAAGTGAATAAAACAAAAAAGTGTAGCACTTAACTCATAC-TACACT
1 GGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTACACC
* * *
395517 GGTGTAAGTGAATAAAATAAAAAAAATGTAGCACTTAACACATTCTTACAAC
1 GGTGTAAGTGAATAAAAT-AAAAAAGTGTAGCACTTAACACATACTTACACC
* * *
395569 GGTATAAGTAAATAAAATAAAAAAGTGTAGCACTTAACACGTACTTACACC
1 GGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTACACC
*
395620 GATGTAAGT
1 GGTGTAAGT
395629 AGGCACATCT
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
50 22 0.16
51 99 0.70
52 20 0.14
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (51 bp):
GGTGTAAGTGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTACACC
Found at i:408779 original size:18 final size:18
Alignment explanation
Indices: 408756--408793 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
408746 TGCGATAATT
408756 GGGCAGTGGTCCAACATG
1 GGGCAGTGGTCCAACATG
*
408774 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAACATG
408792 GG
1 GG
408794 TGGTTGACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (18 bp):
GGGCAGTGGTCCAACATG
Found at i:408915 original size:67 final size:67
Alignment explanation
Indices: 408812--408940 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 67
408802 TGAGCACCTT
* * *
408812 ACAGGATCCTATTGCAGCAGGTTAGATCTGCAGCAGGGCAGCGTAACAGCACTGATCCAGGCACC
1 ACAGGATCCTACTGCAGCAGATAAGATCTGCAGCAGGGCAGCGTAACAGCACTGATCCAGGCACC
408877 CG
66 CG
* * * ***
408879 ACAGGATCCTGCTGCAGCAGATAAGATCTGCTGCAGGGCGGCGTGGTAGCACTGATCCAGGC
1 ACAGGATCCTACTGCAGCAGATAAGATCTGCAGCAGGGCAGCGTAACAGCACTGATCCAGGC
408941 GGATTTCTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.17
Consensus pattern (67 bp):
ACAGGATCCTACTGCAGCAGATAAGATCTGCAGCAGGGCAGCGTAACAGCACTGATCCAGGCACC
CG
Found at i:409235 original size:20 final size:20
Alignment explanation
Indices: 409198--409240 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
409188 GTTCTACCAC
*
409198 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
409218 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
409238 ATG
1 ATG
409241 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:411373 original size:103 final size:103
Alignment explanation
Indices: 411193--411401 Score: 346
Period size: 103 Copynumber: 2.0 Consensus size: 103
411183 ATGGTATACT
* ** *
411193 ATTTTTCCTTAACCAAGGTTTTGTCCCACTTGATTTTTTTGGTAAGGTTTTTAATGAGGCAACAT
1 ATTTTTCCCTAACCAAGGTTTTGTCCCACTTGATTTTCCTGGTAAGATTTTTAATGAGGCAACAT
411258 GTTATACATATTAAAGATATGTGTATTTTTTTCCCTTC
66 GTTATACATATTAAAGATATGTGTATTTTTTTCCCTTC
*
411296 ATTTTTCCCTAACCAAGGTTTTGTCCCACTTGGTTTTCCTGGTAAGATTTTTAATGAGGCAACAT
1 ATTTTTCCCTAACCAAGGTTTTGTCCCACTTGATTTTCCTGGTAAGATTTTTAATGAGGCAACAT
* * *
411361 GTTATGCTTATTAAAGGTATGTGTATTTTTTTCCCTTC
66 GTTATACATATTAAAGATATGTGTATTTTTTTCCCTTC
411399 ATT
1 ATT
411402 AAGATATTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (103 bp):
ATTTTTCCCTAACCAAGGTTTTGTCCCACTTGATTTTCCTGGTAAGATTTTTAATGAGGCAACAT
GTTATACATATTAAAGATATGTGTATTTTTTTCCCTTC
Found at i:411755 original size:2 final size:2
Alignment explanation
Indices: 411744--411800 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
411734 TAGATTATTT
411744 TA TA -A TA TA TA TA TA 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
411785 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
411801 ATTCTCAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:414003 original size:23 final size:23
Alignment explanation
Indices: 413973--414020 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
413963 TCATCACATC
413973 TCAAGTAAAAGCATATTCTCTAT
1 TCAAGTAAAAGCATATTCTCTAT
413996 TCAAGTAAAAGCATATTCTCTAT
1 TCAAGTAAAAGCATATTCTCTAT
414019 TC
1 TC
414021 TCTTGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
TCAAGTAAAAGCATATTCTCTAT
Found at i:424269 original size:20 final size:20
Alignment explanation
Indices: 424246--424283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
424236 AAGAAGGAAC
*
424246 TGAAACTAAACTGAAAATTT
1 TGAAAATAAACTGAAAATTT
*
424266 TGAAAATAACCTGAAAAT
1 TGAAAATAAACTGAAAAT
424284 GATGAACTTG
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:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (20 bp):
TGAAAATAAACTGAAAATTT
Found at i:424289 original size:20 final size:20
Alignment explanation
Indices: 424246--424289 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
424236 AAGAAGGAAC
* **
424246 TGAAACTAAACTGAAAATTT
1 TGAAAATAAACTGAAAATGA
*
424266 TGAAAATAACCTGAAAATGA
1 TGAAAATAAACTGAAAATGA
424286 TGAA
1 TGAA
424290 CTTGCCTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (20 bp):
TGAAAATAAACTGAAAATGA
Found at i:426745 original size:17 final size:17
Alignment explanation
Indices: 426719--426758 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
426709 TAATTCGTAG
*
426719 CTTGCCAGACCATACCT
1 CTTGCGAGACCATACCT
*
426736 CTTGCGAGACTATACCT
1 CTTGCGAGACCATACCT
426753 CTTGCG
1 CTTGCG
426759 GAGTCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.35, G:0.17, T:0.28
Consensus pattern (17 bp):
CTTGCGAGACCATACCT
Found at i:431107 original size:24 final size:22
Alignment explanation
Indices: 431067--431143 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
431057 ATGCAATTAA
431067 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
431086 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
431109 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
431130 TGCATCGATGCACT
1 TGCATCGATGCACT
431144 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:432233 original size:2 final size:2
Alignment explanation
Indices: 432226--432263 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
432216 AGGAAAAATG
432226 AT AT AT AT AT AT AT AT AT AT AT AT AT 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
432264 GAAGATGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:432332 original size:2 final size:2
Alignment explanation
Indices: 432325--432355 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
432315 GAACATGTGA
432325 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 A
432356 GGAAAAGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:432779 original size:23 final size:23
Alignment explanation
Indices: 432746--432813 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
432736 AATCTTATAT
432746 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
432769 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
432792 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
432814 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:437324 original size:2 final size:2
Alignment explanation
Indices: 437317--437379 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
437307 GAACATGTGA
437317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
437359 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
437380 CGATAAGACA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:437805 original size:23 final size:23
Alignment explanation
Indices: 437770--437837 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
437760 AATCTTATAT
437770 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
437793 GGCACTACAGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
437816 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
437838 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:444538 original size:27 final size:27
Alignment explanation
Indices: 444499--444551 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
444489 TTACAAATGA
* *
444499 ATTTTTATCAAATATATAATTTGATAC
1 ATTTTAATCAAATATATAATATGATAC
* *
444526 ATTTTAATTAAATGTATAATATGATA
1 ATTTTAATCAAATATATAATATGATA
444552 TATAAATTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (27 bp):
ATTTTAATCAAATATATAATATGATAC
Found at i:445730 original size:35 final size:34
Alignment explanation
Indices: 445615--445730 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 34
445605 TTAATATATA
* *
445615 ATATC-TTTTAATTTAAATATTTAAAGATATATTG
1 ATATCTTTTTAATTTAAAT-TTTAAAAAGATATTG
* **
445649 ATATCTTTTTAATATTTAAA--ATAAAAAGATAATAA
1 ATATCTTTTT-A-ATTTAAATTTTAAAAAGAT-ATTG
*
445684 ATAT-TTATTAATTTAAATGTTTAAAAAGATATTG
1 ATATCTTTTTAATTTAAAT-TTTAAAAAGATATTG
445718 ATATCTTTTTAAT
1 ATATCTTTTTAAT
445731 ATCTTTTAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
32 7 0.11
33 1 0.02
34 22 0.34
35 26 0.41
36 1 0.02
37 7 0.11
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (34 bp):
ATATCTTTTTAATTTAAATTTTAAAAAGATATTG
Found at i:445768 original size:35 final size:35
Alignment explanation
Indices: 445728--445846 Score: 118
Period size: 35 Copynumber: 3.4 Consensus size: 35
445718 ATATCTTTTT
*
445728 AATATCTTTTAATATTTAAATTTAAAAAGATAATA
1 AATATCTTTTAATATTCAAATTTAAAAAGATAATA
* *
445763 AATATCTTTTACT-TTGAGATATTTAAAATA-AT-ATA
1 AATATCTTTTAATATTCA-A-ATTTAAAA-AGATAATA
* * * *
445798 ATTATCTTATTAATATTCAAATGTAAAGAGATAAGA
1 AATATCTT-TTAATATTCAAATTTAAAAAGATAATA
445834 AATATCTTTTAAT
1 AATATCTTTTAAT
445847 TTAGAATATT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
34 4 0.06
35 36 0.53
36 24 0.35
37 4 0.06
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (35 bp):
AATATCTTTTAATATTCAAATTTAAAAAGATAATA
Found at i:447219 original size:2 final size:2
Alignment explanation
Indices: 447212--447236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
447202 TTATCAATAA
447212 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 A
447237 ATTGAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:449276 original size:2 final size:2
Alignment explanation
Indices: 449269--449331 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
449259 CAAATTAACA
449269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
449311 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
449332 ACCACACTGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:449969 original size:35 final size:34
Alignment explanation
Indices: 449875--450204 Score: 185
Period size: 37 Copynumber: 9.2 Consensus size: 34
449865 AATAATATAG
* ** * *
449875 TATAATTTTTAAAAATGTTTTTGAAAAATATAGTA
1 TATAGTTTTTAAAAA-CATTTTGAAATATATAATA
*
449910 TATAGTTTTTCAAAAACAAATTTTGAAATATATATTA
1 TATAGTTTTT-AAAAAC--ATTTTGAAATATATAATA
* *
449947 TATAGTTTTTTAAAACGTTTTTGAAAACTTATATACAATA
1 TATAGTTTTTAAAAAC-ATTTTG-AAA--TATAT--AATA
*
449987 TATAAG-TTTT-AAAACATTTTGAAAATTATATAGTA
1 TAT-AGTTTTTAAAAACATTTTG-AAA-TATATAATA
* *
450022 TATAG-TTTTGAAATCATTTTGAAA-ATATAATA
1 TATAGTTTTTAAAAACATTTTGAAATATATAATA
*
450054 TATAGTTTTTAAAAAAAACATTTTTAAAAAATTTATATAATA
1 TATAGTTTTT---AAAAACA-TTTT--GAAA--TATATAATA
** ** *
450096 TATAGTTTAAAAAAAACATTTTGAAA-AGCTTATA
1 TATAGTTT-TTAAAAACATTTTGAAATATATAATA
*
450130 TAATA-TTTTTAAAATCAATTTTGAAAACTATATAATA
1 T-ATAGTTTTTAAAAAC-ATTTTG-AAA-TATATAATA
*
450167 TCTAG-TTTTAAAAACATTTT--AA-ATATAATA
1 TATAGTTTTTAAAAACATTTTGAAATATATAATA
450197 TATAGTTT
1 TATAGTTT
450205 AAAAAATATA
Statistics
Matches: 236, Mismatches: 31, Indels: 60
0.72 0.09 0.18
Matches are distributed among these distances:
30 12 0.05
31 2 0.01
32 14 0.06
33 9 0.04
34 24 0.10
35 41 0.17
36 29 0.12
37 44 0.19
38 14 0.06
39 12 0.05
40 17 0.07
41 2 0.01
42 16 0.07
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
TATAGTTTTTAAAAACATTTTGAAATATATAATA
Found at i:450098 original size:74 final size:73
Alignment explanation
Indices: 450008--450244 Score: 204
Period size: 74 Copynumber: 3.2 Consensus size: 73
449998 AAACATTTTG
* * *
450008 AAAATTATATAGTATATAGTTTTGAAATCATTTTGAAAATATAATATATAGTTTTTAAAAAAAAC
1 AAAATTATATAATATATAGTTTTAAAAACATTTTGAAAATATAATATATAGTTTTTAAAAAAAAC
450073 ATTTTTAA
66 ATTTTTAA
* ** *
450081 AAAATTTATATAATATATAGTTTAAAAAAAACATTTTGAAAAGCTTATATAATA-TTTTT---AA
1 AAAA-TTATATAATATATAGTTT--TAAAAACATTTTGAAAATATAATAT-ATAGTTTTTAAAAA
* * *
450142 AATCAATTTT-G
62 AAACATTTTTAA
* * * *
450153 AAAACTATATAATATCTAGTTTTAAAAACATTTT--AAATATAATATATAG--TTTAAAAAATAT
1 AAAATTATATAATATATAGTTTTAAAAACATTTTGAAAATATAATATATAGTTTTTAAAAAAAAC
450214 ATTTTTTGAA
66 A-TTTTT-AA
450224 ACATATATTATATAATATATA
1 A-A-A-ATTATATAATATATA
450245 TTATTATTAA
Statistics
Matches: 127, Mismatches: 23, Indels: 27
0.72 0.13 0.15
Matches are distributed among these distances:
65 3 0.02
66 3 0.02
67 8 0.06
68 4 0.03
69 15 0.12
71 17 0.13
72 5 0.04
73 15 0.12
74 30 0.24
76 24 0.19
77 3 0.02
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (73 bp):
AAAATTATATAATATATAGTTTTAAAAACATTTTGAAAATATAATATATAGTTTTTAAAAAAAAC
ATTTTTAA
Found at i:450108 original size:40 final size:40
Alignment explanation
Indices: 450046--450135 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 40
450036 CATTTTGAAA
*
450046 ATATAATATATAGTTTTTAAAAAAAACATTTTTAAAAAATTT
1 ATATAATATATAG-TTTTAAAAAAAACA-TTTTAAAAAACTT
* *
450088 ATATAATATATAG-TTTAAAAAAAACATTTTGAAAAGCTT
1 ATATAATATATAGTTTTAAAAAAAACATTTTAAAAAACTT
450127 ATATAATAT
1 ATATAATAT
450136 TTTTAAAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 19 0.42
40 13 0.29
42 13 0.29
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (40 bp):
ATATAATATATAGTTTTAAAAAAAACATTTTAAAAAACTT
Found at i:450129 original size:39 final size:38
Alignment explanation
Indices: 449965--450210 Score: 153
Period size: 35 Copynumber: 6.9 Consensus size: 38
449955 TTTAAAACGT
*
449965 TTTTGAAAACTTATATACAATATATAAGTTT---TAAAACA
1 TTTTGAAAACTTATAT--AATATAT-AGTTTAAAAAAAACA
* ** *
450003 TTTTGAAAA-TTATATAGTATATAGTTT--TGAAATCA
1 TTTTGAAAACTTATATAATATATAGTTTAAAAAAAACA
450038 TTTTG-AAA---ATATAATATATAGTTTTTAAAAAAAACA
1 TTTTGAAAACTTATATAATATATAG--TTTAAAAAAAACA
* *
450074 TTTTTAAAAAATTTATATAATATATAGTTTAAAAAAAACA
1 -TTTT-GAAAACTTATATAATATATAGTTTAAAAAAAACA
**
450114 TTTTGAAAAGCTTATATAATAT-T--TTT-AAAATCA-A
1 TTTTGAAAA-CTTATATAATATATAGTTTAAAAAAAACA
* *
450148 TTTTGAAAAC-TATATAATATCTAGTTT--TAAAAACA
1 TTTTGAAAACTTATATAATATATAGTTTAAAAAAAACA
450183 TTTT---AA---ATATAATATATAGTTTAAAAAA
1 TTTTGAAAACTTATATAATATATAGTTTAAAAAA
450211 TATATTTTTT
Statistics
Matches: 173, Mismatches: 17, Indels: 42
0.75 0.07 0.18
Matches are distributed among these distances:
30 15 0.09
32 27 0.16
33 2 0.01
34 24 0.14
35 29 0.17
36 8 0.05
37 10 0.06
38 14 0.08
39 18 0.10
40 13 0.08
42 13 0.08
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (38 bp):
TTTTGAAAACTTATATAATATATAGTTTAAAAAAAACA
Found at i:452835 original size:311 final size:311
Alignment explanation
Indices: 452272--452899 Score: 1256
Period size: 311 Copynumber: 2.0 Consensus size: 311
452262 AACTTGAGGA
452272 CCATAATGGCACTTAGTTCTCAACGGTGGTCCATGATAATAATGCTTCAATTCATTACCGAAACT
1 CCATAATGGCACTTAGTTCTCAACGGTGGTCCATGATAATAATGCTTCAATTCATTACCGAAACT
452337 CACAAGTGTCTTCACCCCGTTGATAAAAGTTGAACCAGTTTTAATTATATAACTTATAATGATTA
66 CACAAGTGTCTTCACCCCGTTGATAAAAGTTGAACCAGTTTTAATTATATAACTTATAATGATTA
452402 ATTTTGATGGTAAATGTCATTCTAATTAAATATCATAATTTCAAAAAGTATCGTTAATGAATCTT
131 ATTTTGATGGTAAATGTCATTCTAATTAAATATCATAATTTCAAAAAGTATCGTTAATGAATCTT
452467 GTTAATGGGACAAAATAAATTATAACAGTTATAGGTAGTTCATTCCTTTAAATTCTGGCGGAATG
196 GTTAATGGGACAAAATAAATTATAACAGTTATAGGTAGTTCATTCCTTTAAATTCTGGCGGAATG
452532 TCATAATCGGTGATAGATTAACCGTTGATTGATTTTAAATTTTTTTTATCT
261 TCATAATCGGTGATAGATTAACCGTTGATTGATTTTAAATTTTTTTTATCT
452583 CCATAATGGCACTTAGTTCTCAACGGTGGTCCATGATAATAATGCTTCAATTCATTACCGAAACT
1 CCATAATGGCACTTAGTTCTCAACGGTGGTCCATGATAATAATGCTTCAATTCATTACCGAAACT
452648 CACAAGTGTCTTCACCCCGTTGATAAAAGTTGAACCAGTTTTAATTATATAACTTATAATGATTA
66 CACAAGTGTCTTCACCCCGTTGATAAAAGTTGAACCAGTTTTAATTATATAACTTATAATGATTA
452713 ATTTTGATGGTAAATGTCATTCTAATTAAATATCATAATTTCAAAAAGTATCGTTAATGAATCTT
131 ATTTTGATGGTAAATGTCATTCTAATTAAATATCATAATTTCAAAAAGTATCGTTAATGAATCTT
452778 GTTAATGGGACAAAATAAATTATAACAGTTATAGGTAGTTCATTCCTTTAAATTCTGGCGGAATG
196 GTTAATGGGACAAAATAAATTATAACAGTTATAGGTAGTTCATTCCTTTAAATTCTGGCGGAATG
452843 TCATAATCGGTGATAGATTAACCGTTGATTGATTTTAAATTTTTTTTATCT
261 TCATAATCGGTGATAGATTAACCGTTGATTGATTTTAAATTTTTTTTATCT
452894 CCATAA
1 CCATAA
452900 GAGGTAGAAC
Statistics
Matches: 317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
311 317 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (311 bp):
CCATAATGGCACTTAGTTCTCAACGGTGGTCCATGATAATAATGCTTCAATTCATTACCGAAACT
CACAAGTGTCTTCACCCCGTTGATAAAAGTTGAACCAGTTTTAATTATATAACTTATAATGATTA
ATTTTGATGGTAAATGTCATTCTAATTAAATATCATAATTTCAAAAAGTATCGTTAATGAATCTT
GTTAATGGGACAAAATAAATTATAACAGTTATAGGTAGTTCATTCCTTTAAATTCTGGCGGAATG
TCATAATCGGTGATAGATTAACCGTTGATTGATTTTAAATTTTTTTTATCT
Found at i:457731 original size:2 final size:2
Alignment explanation
Indices: 457724--457749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
457714 GCATCCCGTC
457724 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
457750 TTTTTTAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458303 original size:2 final size:2
Alignment explanation
Indices: 458296--458367 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
458286 AATTATCCTT
458296 TA TA TA TA TA TA TA TA 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
458338 TA TA 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
458368 AAGGTCAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:459276 original size:2 final size:2
Alignment explanation
Indices: 459269--459293 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
459259 TTAATAAGTT
459269 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 T
459294 TAGTAGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:461070 original size:30 final size:31
Alignment explanation
Indices: 461022--461087 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
461012 TTGACATAAT
*
461022 TAAAA-TAACATAACATAAAATAT-AATACCA
1 TAAAATTAAAATAACAT-AAATATCAATACCA
* *
461052 -AAAATTAAAATAATATAAATTTCAATACCA
1 TAAAATTAAAATAACATAAATATCAATACCA
461082 TAAAAT
1 TAAAAT
461088 ATAATTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 9 0.30
30 16 0.53
31 5 0.17
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (31 bp):
TAAAATTAAAATAACATAAATATCAATACCA
Found at i:468612 original size:21 final size:21
Alignment explanation
Indices: 468551--468624 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
468541 TTTTCATAAT
*
468551 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTAAGTAAA
*
468571 TCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGAATTAAGTAAA
* *
468591 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGTAAA
468612 TCGCAATGCGAAT
1 TCGCAATGCGAAT
468625 ATTACTATCG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 1 0.02
20 25 0.53
21 21 0.45
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGTAAA
Found at i:468635 original size:41 final size:40
Alignment explanation
Indices: 468551--468642 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 40
468541 TTTTCATAAT
* *
468551 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGAATAAGTAAA
* * * *
468591 TCGCAATGCGAATTAGGAAAATCGCAATGCGAAT-ATTACTA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGAATAAGTA-AA
468632 TCGCAATGCGA
1 TCGCAATGCGA
468643 TTTACATAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 15 0.34
41 29 0.66
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGAATAAGTAAA
Found at i:469192 original size:19 final size:19
Alignment explanation
Indices: 469154--469220 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
469144 TTCAAGAATG
469154 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
469174 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
469193 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
469212 AAAATCGCA
1 AAAATCGCA
469221 TTGCAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:469257 original size:14 final size:14
Alignment explanation
Indices: 469238--469326 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
469228 TTTCATTTCG
469238 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
469252 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
469271 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
469285 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
469304 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
469318 CGTTGCGAT
1 CGTTGCGAT
469327 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 30 0.49
16 5 0.08
17 5 0.08
19 21 0.34
ACGTcount: A:0.10, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:469268 original size:33 final size:33
Alignment explanation
Indices: 469230--469350 Score: 215
Period size: 33 Copynumber: 3.6 Consensus size: 33
469220 ATTGCAATTT
**
469230 TCATTTCGCGTTGCGATTCTCTCGTTGCGATTT
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
469263 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
469296 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
469329 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
469351 ATTATCTCGT
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 70 0.82
34 15 0.18
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:469352 original size:20 final size:19
Alignment explanation
Indices: 469216--469375 Score: 107
Period size: 19 Copynumber: 9.1 Consensus size: 19
469206 GAAACCAAAA
* * *
469216 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTCTCATT
469235 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
*
469251 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
469268 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
469284 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
469301 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
469317 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
469334 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
469354 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
469374 TC
1 TC
469376 AACCAAAAGA
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
14 34 0.31
16 3 0.03
17 3 0.03
19 38 0.35
20 30 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:471544 original size:42 final size:42
Alignment explanation
Indices: 471468--471556 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
471458 GACTCGCCTG
* * *
471468 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
471510 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
471552 TCATC
1 TCATC
471557 GTTGAAGTGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:472943 original size:14 final size:14
Alignment explanation
Indices: 472924--472959 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
472914 ATTGTTTAAT
472924 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
472938 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
472952 TGATTTGT
1 TGATTTGT
472960 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:473103 original size:14 final size:14
Alignment explanation
Indices: 473084--473140 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
473074 GCGAAATGAA
473084 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
473098 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
473117 AATCGCAACGAGAG
1 AATCGCAACGAGAG
473131 AATCGCAACG
1 AATCGCAACG
473141 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:473111 original size:33 final size:33
Alignment explanation
Indices: 473066--473155 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
473056 AAAAAGTACT
*
473066 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
473099 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
473132 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
473156 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:473125 original size:19 final size:19
Alignment explanation
Indices: 473066--473126 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
473056 AAAAAGTACT
*
473066 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
473085 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
473099 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
473118 ATCGCAACG
1 ATCGCAACG
473127 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:473173 original size:19 final size:19
Alignment explanation
Indices: 473151--473301 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
473141 CGAAATTAAA
473151 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
473170 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
473185 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
473203 TTCTCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
473217 TTCACGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
473236 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
473251 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
473269 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
473288 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
473302 AGACATTAAG
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 46 0.49
20 9 0.10
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:473197 original size:33 final size:32
Alignment explanation
Indices: 473155--473281 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
473145 ATTAAATTCG
473155 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* *
473188 CGTTGCGATTTTCATTTCTCATTGCGAAATT-CA
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
473221 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
473254 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
473282 AGTAATTTCT
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:473231 original size:66 final size:66
Alignment explanation
Indices: 473148--473280 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
473138 ACGCGAAATT
* *
473148 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCTCATTGC
1 AAATTCACGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
473213 G
66 G
* *
473214 AAATTCACGTTGTGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCACGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
473279 G
66 G
473280 A
1 A
473281 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.43
Consensus pattern (66 bp):
AAATTCACGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:475590 original size:12 final size:12
Alignment explanation
Indices: 475573--475597 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
475563 TCTTCGGGGA
475573 CTTTTTCTTCTT
1 CTTTTTCTTCTT
475585 CTTTTTCTTCTT
1 CTTTTTCTTCTT
475597 C
1 C
475598 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:475806 original size:24 final size:24
Alignment explanation
Indices: 475772--475825 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
475762 CTGAAACATC
*
475772 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
475796 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
475820 ATCAAA
1 ATCAAA
475826 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:476735 original size:20 final size:19
Alignment explanation
Indices: 476688--476737 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
476678 GAGATAATAC
476688 AAAATCGCAACGAGATTCT
1 AAAATCGCAACGAGATTCT
**
476707 AACTTTCGCAACGAGATTCT
1 AA-AATCGCAACGAGATTCT
476727 GAAAATCGCAA
1 -AAAATCGCAA
476738 TCATCTTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (19 bp):
AAAATCGCAACGAGATTCT
Found at i:477046 original size:20 final size:20
Alignment explanation
Indices: 476951--477038 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
476941 CAACGGGGAA
476951 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
476971 ATCGCAACACGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
476991 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
477011 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
477031 ATCGCAAC
1 ATCGCAAC
477039 TAGAAAATCG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 5 0.09
20 45 0.82
21 5 0.09
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:477106 original size:19 final size:19
Alignment explanation
Indices: 477065--477151 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
477055 GAAATGAAAA
477065 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
477081 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
477098 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
477117 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
477136 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
477152 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:477135 original size:38 final size:33
Alignment explanation
Indices: 477065--477161 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 33
477055 GAAATGAAAA
477065 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
477098 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
477136 TCGCATTGCGATTTTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
477162 AGTCAGTTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
33 23 0.39
35 3 0.05
36 3 0.05
38 30 0.51
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:477317 original size:13 final size:13
Alignment explanation
Indices: 477288--477325 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
477278 CACCAATTAA
*
477288 ACAAATCAACATTT
1 ACAAATCAA-TTTT
477302 ACAAATCAATTTT
1 ACAAATCAATTTT
477315 ACAAATCAATT
1 ACAAATCAATT
477326 AAACAATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:477331 original size:13 final size:13
Alignment explanation
Indices: 477281--477335 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
477271 ATGTACACAC
477281 CAATTAAACAAAT
1 CAATTAAACAAAT
*
477294 CAACATT-TACAAAT
1 C-A-ATTAAACAAAT
**
477308 CAATTTTACAAAT
1 CAATTAAACAAAT
477321 CAATTAAAC-AAT
1 CAATTAAACAAAT
477333 CAA
1 CAA
477336 AAAATAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 9 0.25
13 16 0.44
14 8 0.22
15 3 0.08
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (13 bp):
CAATTAAACAAAT
Found at i:478788 original size:40 final size:42
Alignment explanation
Indices: 478735--478821 Score: 115
Period size: 40 Copynumber: 2.1 Consensus size: 42
478725 CCTCTTCAAC
* * *
478735 AATGACAGTGGCCTCTTGAACG-GTGG-GGGGACTCTTGAGG
1 AATGATAGGGGCCTCTTGAACGAGTGGAGAGGACTCTTGAGG
* *
478775 GATGATAGGGGCCTCTTGAACGATTGGAGAGGACTCTTGAGG
1 AATGATAGGGGCCTCTTGAACGAGTGGAGAGGACTCTTGAGG
478817 AATGA
1 AATGA
478822 CAGGTGAGTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 19 0.49
41 3 0.08
42 17 0.44
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.23
Consensus pattern (42 bp):
AATGATAGGGGCCTCTTGAACGAGTGGAGAGGACTCTTGAGG
Found at i:479189 original size:20 final size:20
Alignment explanation
Indices: 479164--479201 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
479154 AATAATAGTT
479164 TACTTTCGCAACACGAAACC
1 TACTTTCGCAACACGAAACC
*
479184 TACTTTCGCAACGCGAAA
1 TACTTTCGCAACACGAAA
479202 ATGACTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.13, T:0.21
Consensus pattern (20 bp):
TACTTTCGCAACACGAAACC
Found at i:479212 original size:20 final size:20
Alignment explanation
Indices: 479189--479261 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
479179 AAACCTACTT
479189 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
479209 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
479229 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
479249 TCGCAATGCGAAA
1 TCGCAACGCGAAA
479262 TGAAAATCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:479275 original size:39 final size:40
Alignment explanation
Indices: 479192--479275 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
479182 CCTACTTTCG
** *
479192 CAACGCGAAAATGACTATCGCAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCGCAACGCGGAAATGAAAATCA
* * *
479232 CAACGCGGAAATGGCTATCGCAATGC-GAAATGAAAATCA
1 CAACGCGAAAATGACTATCGCAACGCGGAAATGAAAATCA
479271 CAACG
1 CAACG
479276 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (40 bp):
CAACGCGAAAATGACTATCGCAACGCGGAAATGAAAATCA
Found at i:479316 original size:14 final size:14
Alignment explanation
Indices: 479264--479322 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
479254 ATGCGAAATG
*
479264 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
479278 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
479297 AAAATCGCAACGAC
1 AAAATCGCAACGAC
479311 AAAATCGCAACG
1 AAAATCGCAACG
479323 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:479336 original size:33 final size:33
Alignment explanation
Indices: 479248--479339 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
479238 GGAAATGGCT
*
479248 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
479281 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
479314 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
479340 TGCGATTTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:479373 original size:14 final size:14
Alignment explanation
Indices: 479351--479414 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 14
479341 GCGATTTGTG
479351 TTTTG-CGTTGCGA
1 TTTTGTCGTTGCGA
479364 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
*
479378 TTTTCATTTCGCATTGCGA
1 -TTT--TGTCG--TTGCGA
479397 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
479411 TTTT
1 TTTT
479415 CATTTCGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
13 5 0.12
14 18 0.42
15 3 0.07
16 4 0.09
17 4 0.09
18 3 0.07
19 6 0.14
ACGTcount: A:0.09, C:0.16, G:0.23, T:0.52
Consensus pattern (14 bp):
TTTTGTCGTTGCGA
Found at i:479394 original size:19 final size:19
Alignment explanation
Indices: 479372--479430 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
479362 GATTTTGTCG
479372 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
479391 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
479405 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
479424 TTGCGAT
1 TTGCGAT
479431 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 13 0.39
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:479395 original size:33 final size:33
Alignment explanation
Indices: 479358--479430 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
479348 GTGTTTTGCG
479358 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
479391 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
479424 TTGCGAT
1 TTGCGAT
479431 AGCCATTTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:479449 original size:20 final size:19
Alignment explanation
Indices: 479415--479469 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
479405 TTGCGATTTT
*
479415 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
479434 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
479454 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
479470 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:480033 original size:18 final size:18
Alignment explanation
Indices: 480010--480057 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
480000 CGGGTCGATC
480010 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
480028 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
480046 AGGTGATGGCTC
1 AGGTGATGGCTC
480058 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:481425 original size:20 final size:20
Alignment explanation
Indices: 481377--481435 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
481367 AATAGTTTCT
* *
481377 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
481397 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
481417 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
481436 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:481711 original size:22 final size:22
Alignment explanation
Indices: 481684--481727 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
481674 GATGGAGATA
*
481684 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
481706 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
481728 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:482013 original size:41 final size:41
Alignment explanation
Indices: 481894--482072 Score: 155
Period size: 41 Copynumber: 4.4 Consensus size: 41
481884 CGCTTTGAAA
* * *
481894 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
481935 ATTGAGTTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
481975 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
482016 ACCGCGTTGTGATTTTCCA-AATTCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTA-TCGCGTTGCGAAAGTCAGT
* *
482057 ATCACATTGCGATTTT
1 ATCGCGTTGCGATTTT
482073 CCAAATTTGC
Statistics
Matches: 108, Mismatches: 28, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 33 0.31
41 75 0.69
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:482023 original size:20 final size:20
Alignment explanation
Indices: 481914--482024 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
481904 GATTATGTAT
*
481914 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
481934 TATTGAGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
481954 TATCGAGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
481974 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
481995 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
482015 TACCGCGTTG
1 TATCGCGTTG
482025 TGATTTTCCA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.04
20 54 0.74
21 14 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:482073 original size:41 final size:41
Alignment explanation
Indices: 481961--482086 Score: 146
Period size: 41 Copynumber: 3.1 Consensus size: 41
481951 AAGTATCGAG
* ** * *
481961 TTGCGAAAGTCAGTATCGCGTTGCGATTTT-GTATTATCGCG
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
* *
482002 TTGCGATAGTCAGTACCGCGTTGTGATTTTCCAAATTCGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
* * *
482043 TTGCGATAGTCAGTATCACATTGCGATTTTCCAAATTTGCA
1 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
482084 TTG
1 TTG
482087 TGATTTACTT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 70 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAATTCGCA
Found at i:482151 original size:21 final size:22
Alignment explanation
Indices: 482102--482151 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
482092 TACTTATTCG
*
482102 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCA
**
482123 CAACGCGAAATT-GGAAAATCA
1 CATTGCGAAATTGGGAAAATCA
482144 CATTGCGA
1 CATTGCGA
482152 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCA
Found at i:495803 original size:8 final size:7
Alignment explanation
Indices: 495779--495820 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
495769 TTTTCATACA
495779 TGCA-TT
1 TGCATTT
495785 TGCATTT
1 TGCATTT
495792 TGCATCTT
1 TGCAT-TT
495800 TGCATTT
1 TGCATTT
* *
495807 TTCATTG
1 TGCATTT
495814 TGCATTT
1 TGCATTT
495821 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:495803 original size:15 final size:14
Alignment explanation
Indices: 495779--495820 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
495769 TTTTCATACA
495779 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
495792 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
495807 TTCATTGTGCATTT
1 TGCATTTTGCATTT
495821 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:495909 original size:26 final size:25
Alignment explanation
Indices: 495880--495937 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
495870 CATTCACATA
*
495880 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTT-CATT
* *
495906 TTTACGTTTGTATTTACATTTCATT
1 TTTACATTTGAATTTACATTTCATT
495931 TTTACAT
1 TTTACAT
495938 AATTACATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTACATTTGAATTTACATTTCATT
Found at i:497928 original size:10 final size:9
Alignment explanation
Indices: 497907--497982 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
497897 CAAAGAAAGG
497907 AAAAA-AGA
1 AAAAAGAGA
497915 AAAAAGAGGA
1 AAAAAGA-GA
*
497925 AAAAAGAAA
1 AAAAAGAGA
497934 AAAAAG-GA
1 AAAAAGAGA
*
497942 AAGAAATAGA
1 AA-AAAGAGA
497952 AAAAA-A-A
1 AAAAAGAGA
*
497959 ACAAAAAAG-
1 A-AAAAGAGA
*
497968 AAAAAGAAA
1 AAAAAGAGA
497977 AAAAAG
1 AAAAAG
497983 TAAATCAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
7 2 0.04
8 18 0.33
9 22 0.40
10 13 0.24
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:497952 original size:20 final size:17
Alignment explanation
Indices: 497902--497972 Score: 88
Period size: 17 Copynumber: 4.0 Consensus size: 17
497892 TCCAGCAAAG
497902 AAAGGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
*
497919 AGAGGAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
497936 AAAGGAAAGAAATAGAAAAA
1 AAAGG-AA-AAA-AGAAAAA
**
497956 AAAACAAAAAAGAAAAA
1 AAAGGAAAAAAGAAAAA
497973 GAAAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
17 27 0.57
18 5 0.11
19 5 0.11
20 10 0.21
ACGTcount: A:0.80, C:0.01, G:0.17, T:0.01
Consensus pattern (17 bp):
AAAGGAAAAAAGAAAAA
Found at i:497981 original size:17 final size:17
Alignment explanation
Indices: 497907--497981 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 17
497897 CAAAGAAAGG
497907 AAAAAAGAAAAAAGAGGAAA
1 AAAAAAG-AAAAAGA--AAA
*
497927 AAAGAAA-AAAAAGGAAA
1 AAA-AAAGAAAAAGAAAA
* *
497944 GAAATAGAAAAA-AAAA
1 AAAAAAGAAAAAGAAAA
497960 CAAAAAAGAAAAAGAAAA
1 -AAAAAAGAAAAAGAAAA
497978 AAAA
1 AAAA
497982 GTAAATCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 4 0.09
19 6 0.13
20 3 0.07
21 3 0.07
ACGTcount: A:0.83, C:0.01, G:0.15, T:0.01
Consensus pattern (17 bp):
AAAAAAGAAAAAGAAAA
Found at i:503034 original size:22 final size:22
Alignment explanation
Indices: 503003--503055 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
502993 ATCTACACTC
**
503003 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
503025 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
503047 TTCAAAGAT
1 TTCAAAGAT
503056 AAAAGCTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:503654 original size:113 final size:113
Alignment explanation
Indices: 503457--504003 Score: 676
Period size: 112 Copynumber: 4.9 Consensus size: 113
503447 TTAGCAAAGT
* *
503457 TCAAATCCATCATTCAATGGATCAACA-TTCCAG-GACGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGA-GAGTTCATAATGAGAAGAACTCATCTG
* *
503520 AATAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
503569 TCAAATCCATCATTCGATTGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
503634 AGAAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * ** *
503682 TTAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
* *
503747 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* ** * * * * **
503794 TTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
*
503859 AG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-C
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *** * *
503905 CCTGAATTCATCACTT-GATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TC-AAATTCATCA-TTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCT
*
503969 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTT
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTT
504004 ATCTGAAGAG
Statistics
Matches: 382, Mismatches: 48, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
111 2 0.01
112 242 0.63
113 136 0.36
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATTCATCATTCGATGGATCAACATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:503980 original size:19 final size:19
Alignment explanation
Indices: 503956--504019 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
503946 TTCATAATGA
503956 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
**
503975 GAAGAA-GAAGTTCAT-AATGA-
1 GAAGAACTTA--TC-TGAA-GAG
503995 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
504014 GAAGAA
1 GAAGAA
504020 GAAGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAGAACTTATCTGAAGAG
Found at i:503982 original size:22 final size:22
Alignment explanation
Indices: 503955--504022 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
503945 GTTCATAATG
503955 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
503977 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
503994 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
504016 AGAAGAA
1 AGAAGAA
504023 GTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 7 0.20
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:503997 original size:39 final size:39
Alignment explanation
Indices: 503943--504042 Score: 200
Period size: 39 Copynumber: 2.6 Consensus size: 39
503933 TTTCCAGAGA
503943 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
503982 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
504021 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
504043 GTTTAACCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:504001 original size:151 final size:151
Alignment explanation
Indices: 503832--504151 Score: 534
Period size: 151 Copynumber: 2.1 Consensus size: 151
503822 TGCCAGTTAG
*
503832 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
***
503897 ACCTTTTCC-CTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTCCTC-GAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
503961 ACTTATCTGAAGAGGAAGAAGA
130 ACTTATCTGAAGAGGAAGAAGA
* * *
503983 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* *
504048 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
504113 CTTATCTGAAGAGGAAGAAGA
131 CTTATCTGAAGAGGAAGAAGA
*
504134 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
504152 TTTGTTTAAC
Statistics
Matches: 158, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
151 157 0.99
152 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGA
Found at i:504021 original size:263 final size:264
Alignment explanation
Indices: 503720--504263 Score: 840
Period size: 263 Copynumber: 2.1 Consensus size: 264
503710 TACCAGTTAG
*
503720 AGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * ** *
503785 ACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
503850 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
* * * *
503915 TCACTTGATGAATT-ATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG-AAGAGGAA
196 TCACTTGATGAATTAACTTTTT-CAGAGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGGAA
503978 GAAGA
260 GAAGA
* * *
503983 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * * *
504048 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
* * *
504113 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
*
504178 TCACTTGATGGATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGGAAG
196 TCACTTGATGAATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGGAAG
504243 AAGA
261 AAGA
504247 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
504264 GCTTGTTCAA
Statistics
Matches: 254, Mismatches: 25, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
263 219 0.86
264 35 0.14
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (264 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
TCACTTGATGAATTAACTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAAAAGGAAG
AAGA
Found at i:504179 original size:112 final size:112
Alignment explanation
Indices: 503982--504270 Score: 481
Period size: 112 Copynumber: 2.6 Consensus size: 112
503972 GAGGAAGAAG
503982 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
504047 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
66 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
* *
504094 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
* *
504159 AACCTTTTGC-CTGAATTCATCACTTGATGGATTAACTTTTTCAGAGA
66 AACCTTTTGCTC-GAATTCATCACTTGATGGATTAACATTTCCAGAGA
* * * *
504206 AAGTTCATAATGAGAAGAACTCATATGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTG-AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
504271 CAACATTTGT
Statistics
Matches: 165, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
111 1 0.01
112 131 0.79
113 33 0.20
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
Found at i:505736 original size:30 final size:30
Alignment explanation
Indices: 505691--505751 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
505681 TAATATAATT
* *
505691 TTATTTTAATCATTATTTATTTTTA-TATG
1 TTATTTTAATCATTATTGATTATTATTATG
*
505720 TTATATTTAATTATTATTGATTATTATTATG
1 TTAT-TTTAATCATTATTGATTATTATTATG
505751 T
1 T
505752 ATCATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 18 0.67
31 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (30 bp):
TTATTTTAATCATTATTGATTATTATTATG
Found at i:512571 original size:16 final size:16
Alignment explanation
Indices: 512550--512581 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
512540 CATATAGCAG
512550 GTAAAAATATGATAAA
1 GTAAAAATATGATAAA
512566 GTAAAAATATGATAAA
1 GTAAAAATATGATAAA
512582 ACCGATGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (16 bp):
GTAAAAATATGATAAA
Found at i:512873 original size:182 final size:181
Alignment explanation
Indices: 512566--513183 Score: 796
Period size: 182 Copynumber: 3.4 Consensus size: 181
512556 ATATGATAAA
* * * ** * *
512566 GTAAAAATATGATAAAACCGATGTC-ATTATGATAAAATAGGTAAACCGCTACCGGTTATATTAA
1 GTAAAAATATGACAAAACCGGTGTCGA-AATGATAAAACCGGTAAAACGCTACCGGATATATTAA
*
512630 AAGTGTCGATAAATTAATATAAGTATCGACACTTTTGTAATTTAAAAGAGAAGAAGTTATAGCGC
65 AAGTGTCGATAAATTAATATAAGTATCGACACTTTT-TAATTTAAAAGAGAAAAAGTTATAGCGC
*
512695 CTATAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
129 CTAAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
* * *
512748 GTAAAAATATGATAAAACCGGTGTC-ATTATGATAAAACCGGTAAACCGCTACCGGATATATTAA
1 GTAAAAATATGACAAAACCGGTGTCGA-AATGATAAAACCGGTAAAACGCTACCGGATATATTAA
* *
512812 AAGTGCCGATAAATTAATATAAGTATCGACACTTTTTATATTTAAAAGAGAAAAAGTTATAGCGT
65 AAGTGTCGATAAATTAATATAAGTATCGACACTTTTTA-ATTTAAAAGAGAAAAAGTTATAGCGC
* * *
512877 CTAAAAAGTGTCGATATTTTATACAAATGTATCGATCCATAGCAATATAACAT
129 CTAAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
* * * * ** ** * *
512930 GTAATAATATGACAAAACAGGTCTCGAAATGAAAAAAAGGGTAAAAAACTACCAGATATATTGAA
1 GTAAAAATATGACAAAACCGGTGTCGAAATGATAAAACCGGTAAAACGCTACCGGATATATTAAA
*
512995 AGTGTCGATAAATTAATATAAGTATCGACACTTTCGTAATTTAAAAGAGAAGAAA-TTATAGCGC
66 AGTGTCGATAAATTAATATAAGTATCGACACTTT-TTAATTTAAAAGAGAA-AAAGTTATAGCGC
* * *
513059 CTAAAAAGTATCGATACTTTATGA-AAATGTATCTATCCATA-ACAATATAATAG
129 CTAAAAAGTGTCGATACTTTAT-ACAAATGTATCGATCCATAGA-AATATAACAG
* * * * * *
513112 GTAAAAATATGACAAAATCGGTATCGAAATGACAAAACCGGTAAAACGCTACCGGTTATGTTGAA
1 GTAAAAATATGACAAAACCGGTGTCGAAATGATAAAACCGGTAAAACGCTACCGGATATATTAAA
513177 AGTGTCG
66 AGTGTCG
513184 GTACTTTAAT
Statistics
Matches: 385, Mismatches: 45, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
181 2 0.01
182 376 0.98
183 7 0.02
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
GTAAAAATATGACAAAACCGGTGTCGAAATGATAAAACCGGTAAAACGCTACCGGATATATTAAA
AGTGTCGATAAATTAATATAAGTATCGACACTTTTTAATTTAAAAGAGAAAAAGTTATAGCGCCT
AAAAAGTGTCGATACTTTATACAAATGTATCGATCCATAGAAATATAACAG
Found at i:515090 original size:22 final size:22
Alignment explanation
Indices: 515039--515094 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
515029 GTTTTTTGGT
*
515039 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
515062 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
515085 TTTTATTATA
1 TTTTATTATA
515095 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:515397 original size:15 final size:15
Alignment explanation
Indices: 515374--515403 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
515364 TTGGAGGGGT
515374 GGATGACGGTCAGGG
1 GGATGACGGTCAGGG
*
515389 GGATTACGGTCAGGG
1 GGATGACGGTCAGGG
515404 AAAACAGAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.50, T:0.17
Consensus pattern (15 bp):
GGATGACGGTCAGGG
Found at i:515782 original size:18 final size:18
Alignment explanation
Indices: 515759--515797 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
515749 GAGAAAATTT
*
515759 GAAGAAGAAAAGATGGAG
1 GAAGAAAAAAAGATGGAG
515777 GAAGAAAAAAAGATGGAG
1 GAAGAAAAAAAGATGGAG
515795 GAA
1 GAA
515798 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (18 bp):
GAAGAAAAAAAGATGGAG
Found at i:517291 original size:19 final size:19
Alignment explanation
Indices: 517267--517316 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
517257 AAATGTAGGG
517267 TTAATTTTGTATAAG-TTT
1 TTAATTTTGTATAAGATTT
*
517285 CTTAATTTTGTATACGATTT
1 -TTAATTTTGTATAAGATTT
*
517305 ATAATTTTGTAT
1 TTAATTTTGTAT
517317 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 25 0.89
20 3 0.11
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:517966 original size:198 final size:197
Alignment explanation
Indices: 517458--518393 Score: 1500
Period size: 198 Copynumber: 4.7 Consensus size: 197
517448 TATTCCAAGT
* **
517458 ATACTTTGTGTCCATAATGATTTCCTTACCAA-GTGCATGGA-AATGTGTCGATACATTTATAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGT-CA-CCACAATGTGTCGATACATTTATAAA
* * *
517521 ATGTATCGATCCAAAAAATATCGAGACCCATAATTATAATCTAATAGGTAAATTATCAATCTAAC
64 AAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAAC
* *
517586 CGGTCTAAATATACCGGTTTATGAGAAAACAGGTGTACATAAAGTATCGACACTTGTTTAATTTG
129 CGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTT-TTTAATTTG
517651 TGTCG
193 TGTCG
* * *
517656 ATCCCGTACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCATAATGTGTTGATACCTTTAT
1 A-----TACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTAT
*
517721 AAAAAGTATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
61 AAAAAGTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCT
* * * *
517786 AACCGGTCTAAACACACCGGTTTATAAGAAAACAAGTGTACATGAAGTATCGACACGTTTTGAAT
126 AACCGGTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACAC-TTTTTAAT
517851 TTGTGTCG
190 TTGTGTCG
*
517859 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTTACCACAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
*
517924 ATATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
* *
517989 GTCTAAATACACCGGTTTTTGAGAAAACAGGTGTACATGAAGTATCGACACTCTTTCAATTTGTG
131 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACT-TTTTAATTTGTG
518054 TCG
195 TCG
518057 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
*
518122 GTATCGATCCAAAAAATATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
*
518187 GTCTAAATAAACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACCTTTTTAATTTGTG
131 GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACA-CTTTTTAATTTGTG
518252 TCG
195 TCG
*
518255 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGCTACATTTATAAAAA
1 ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
* *
518320 GTATCGATCCAAAAAACATCGAGACCCATAAATATAATGTAATAGGTAAATT-TGCAATGTAACC
66 GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTAT-CAATCTAACC
* *
518384 AGTATAAATA
130 GGTCTAAATA
518394 TACCTATTTA
Statistics
Matches: 689, Mismatches: 38, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
197 2 0.00
198 505 0.73
199 2 0.00
202 1 0.00
203 175 0.25
204 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (197 bp):
ATACTTTGTGTCCAGAATGATTTCCTTACCAAGGTCACCACAATGTGTCGATACATTTATAAAAA
GTATCGATCCAAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATCAATCTAACCG
GTCTAAATACACCGGTTTATGAGAAAACAGGTGTACATGAAGTATCGACACTTTTTAATTTGTGT
CG
Found at i:518778 original size:15 final size:15
Alignment explanation
Indices: 518757--518794 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
518747 CATAGTCGGG
518757 GCTCTTCTCAACCCA
1 GCTCTTCTCAACCCA
*
518772 TCTCTTCTCAACCCA
1 GCTCTTCTCAACCCA
518787 GCTCTTCT
1 GCTCTTCT
518795 GAGGAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (15 bp):
GCTCTTCTCAACCCA
Found at i:519952 original size:12 final size:12
Alignment explanation
Indices: 519918--519955 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
519908 CAAGCGGTCA
*
519918 ATGAAGATGACG
1 ATGAAGATGATG
519930 ATGAAGATGATG
1 ATGAAGATGATG
*
519942 ATGATGATGATG
1 ATGAAGATGATG
519954 AT
1 AT
519956 CCAAACAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (12 bp):
ATGAAGATGATG
Found at i:522128 original size:201 final size:198
Alignment explanation
Indices: 521771--522804 Score: 1324
Period size: 198 Copynumber: 5.2 Consensus size: 198
521761 AATTCAAAAA
* **
521771 TATCGACACTTTATACATTTGTGTCGATACTTTGTGTCCATAATGTATTTTCCAACCAAAACAAG
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTT----CC-AAACAAG
* * * * *
521836 TTCAC-AAATAAGTGTCGACACATTTATATCAAGTGTCGATCCCAAAAACATCGAAACTCGTAAC
61 TTCACGAAA-AAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAAT
* * * * * * * * *
521900 TATAACGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCAGTT-TTATGAGAAAATAG
125 TATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTA--A-AAAAAAG
*
521964 GTCTACA-ATATG
187 GTATACATA-ATG
* * * ** *
521976 TATCGACACTTTATTCATTTGTGTCGATACATGT-TGTCCAGAATGTA-TTTCCAAACCAAGTGC
1 TATCGACACTTTATACATTTGTGTCGATAC-TTTATGTCCATAATAAATTTTCCAAA-CAAGTTC
*
522039 ACGAAAAAAGTGTCGATACATTTATACCAAGTGTCGATCCCAAAAACATCGAAACACATAATTAT
64 ACG-AAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTAT
522104 AATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAGAAAGGTAT
128 AATGTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATT-AAAAA-AAAGGTAT
522169 ACATAATG
191 ACATAATG
* * *
522177 TATCGATACTTTATACATTTGTGTCTACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
522242 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* * * *
522307 GTAAAAGGTAATATAACAATGTAACCGGTCTAAACATACCGGTTATTAAAAAAAAGGTATACGTA
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATA
522372 ATG
196 ATG
* *
522375 TATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
*
522440 GAAAAAGTGTCGATATATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* * *
522505 GTAATAGGTAATATAACAATGTAACCGGTCTAAACATACCGGTTATTAAAAAAAAGGTATACGTA
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATA
522570 ATG
196 ATG
* *
522573 TATCGATACTTTATACATTTGTGTCGACACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
1 TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
* * * * *
522638 GAAAAAGTGTCAATACATTTATAAAAAGTGTCGATCCTAAAAACATCGAAACCCGTAATTATAAT
66 GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
* * * * * * * * * * * * *
522703 GTAATAGATCACTTTACAATGTAACCAGT-TTAATTTTCTGGTTTCATGAGAAAATAGGTCTACA
131 GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGG-TT-ATTAAAAAAAAGGTATACA
522767 TAATG
194 TAATG
* * *
522772 CATCGACACTTTTTAAATTTGTGTCGATACTTT
1 TATCGACACTTTATACATTTGTGTCGATACTTT
522805 TTAAAATTAC
Statistics
Matches: 754, Mismatches: 63, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
197 7 0.01
198 359 0.48
199 55 0.07
200 122 0.16
201 150 0.20
202 14 0.02
203 1 0.00
204 3 0.00
205 41 0.05
206 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (198 bp):
TATCGACACTTTATACATTTGTGTCGATACTTTATGTCCATAATAAATTTTCCAAACAAGTTCAC
GAAAAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACACATAATTATAAT
GTAATAGGTAACATAACAATGTAACCGGTCTAAATATACCGGTTATTAAAAAAAAGGTATACATA
ATG
Found at i:526359 original size:198 final size:196
Alignment explanation
Indices: 525953--526470 Score: 558
Period size: 198 Copynumber: 2.6 Consensus size: 196
525943 ATTAAATTTT
* * * ** *
525953 GTGTCGATACATTTATAACAAGTATCGATCCCAAAATCAAAGAGACCGATAATTATAATGTAATA
1 GTGTCGATACATTT-TAAAAATTATCGATCCCGAAA-CATCGAAACCGATAATTATAATGTAATA
* * *
526018 GGTAAATTTTCAATGTAACCAG-TAGAAATATACCGGGTTCATGAGAGAATAGGTCAACAATATG
64 GGTAAATTTACAATGTAACCGGTTA-AAATATACC-GGTTAATGAGAGAATAGGTCAACAATATG
* * * * *** *
526082 TATCAACACTTTTTTAATTTGTGTCGATACATTTTTCCAAAATGAATGGCAAACGAGGTGTACGC
127 TATCAACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAACACAAACGAGGTGCACGC
526147 ATAAA
192 ATAAA
* * *
526152 GTGTCGATACATTTGTAAAAATTATCGATCCTCGAAACATCGAAATCGATAATTATTATGTAACA
1 GTGTCGATACATTT-TAAAAATTATCGATCC-CGAAACATCGAAACCGATAATTATAATGTAATA
* * *
526217 GGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATTAGCA-AATAGGTCTACATTATGT
64 GGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAG-AGAATAGGTCAACAATATGT
*** * * *
526281 ATCGGTACTCTTTAAATATGTGTCGATACTTTTTTCCAAAATAAAACACAAACGAGTTGCATGCA
128 ATCAACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAACACAAACGAGGTGCACGCA
526346 TAAA
193 TAAA
* *
526350 GTGTCGATACA-TTTAAAATTGTATCGATCCCGAAAACATCGAAACCGAT-ATACATAATGTAAT
1 GTGTCGATACATTTTAAAAAT-TATCGATCCCG-AAACATCGAAACCGATAAT-TATAATGTAAT
* * * * * * * *
526413 AGGTCAATTTATAATGTAACCGGTTTAAATTTACTGGTTTTATGAGAAAATATGTCAA
63 AGGTAAATTTACAATGTAACCGGTTAAAATATACCGG-TTAATGAGAGAATAGGTCAA
526471 TATAAGCGCT
Statistics
Matches: 267, Mismatches: 44, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
196 10 0.04
197 67 0.25
198 104 0.39
199 80 0.30
200 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTTAAAAATTATCGATCCCGAAACATCGAAACCGATAATTATAATGTAATAGG
TAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAGAGAATAGGTCAACAATATGTATC
AACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAAACACAAACGAGGTGCACGCATAA
A
Found at i:526996 original size:18 final size:19
Alignment explanation
Indices: 526954--526997 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
526944 TAGGGTTCAC
* *
526954 GGAATATAAGATTATCAGT
1 GGAATAAAAGATTACCAGT
526973 GAGAATAAAAGATTACCAG-
1 G-GAATAAAAGATTACCAGT
526992 GGAATA
1 GGAATA
526998 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGT
Found at i:527184 original size:36 final size:39
Alignment explanation
Indices: 527135--527212 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 39
527125 ATAATATTAC
527135 AAATTGTAAAATATTTATAT-A-TTTTCTTTAAAAAATT
1 AAATTGTAAAATATTTATATAATTTTTCTTTAAAAAATT
* * *
527172 AAATT-TATAATATTTATATAATTTTTTTTTACAAAATT
1 AAATTGTAAAATATTTATATAATTTTTCTTTAAAAAATT
527210 AAA
1 AAA
527213 ATATAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 13 0.36
37 6 0.17
38 17 0.47
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (39 bp):
AAATTGTAAAATATTTATATAATTTTTCTTTAAAAAATT
Found at i:531021 original size:19 final size:21
Alignment explanation
Indices: 530984--531026 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
530974 CACTCACTAC
530984 TGTATTACTTGCATCGA-TTG
1 TGTATTACTTGCATCGATTTG
531004 TGTA-TACTTGCA-CAGATTTG
1 TGTATTACTTGCATC-GATTTG
531024 TGT
1 TGT
531027 GCCACATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.05
19 10 0.48
20 10 0.48
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (21 bp):
TGTATTACTTGCATCGATTTG
Found at i:533967 original size:37 final size:37
Alignment explanation
Indices: 533895--534286 Score: 377
Period size: 38 Copynumber: 10.7 Consensus size: 37
533885 TAGTTTTTGT
533895 TTTTTAAAAAATCACTTTTG-AAATATATAT--TATATAG
1 TTTTT-AAAAA-CA-TTTTGAAAATATATATAATATATAG
*
533932 -TTTTGAAAACATTTTTGAAAATATATATAATATATAG
1 TTTTTAAAAACA-TTTTGAAAATATATATAATATATAG
* ** * *
533969 TTTTGAAAATGATTTTTGAAAATGTATATATTATATAG
1 TTTTTAAAAACA-TTTTGAAAATATATATAATATATAG
** *
534007 TTTTTCGAAACATTTTGAAAACT-TATATAATATATGG
1 TTTTTAAAAACATTTTGAAAA-TATATATAATATATAG
*
534044 TTTTTAAAAACATTTT-AAAAAATATATAATATAT-G
1 TTTTTAAAAACATTTTGAAAATATATATAATATATAG
*
534079 TTTTTAAAAACATTTTGAAAA-ATTATATAATATATGG
1 TTTTTAAAAACATTTTGAAAATA-TATATAATATATAG
*
534116 TTTTTAAAAAACATTTTGAAAACT-TATATAATATATGG
1 TTTTT-AAAAACATTTTGAAAA-TATATATAATATATAG
534154 TTTTTTAAAAAACATTTTGAAAATATATATAATATAT-G
1 -TTTTT-AAAAACATTTTGAAAATATATATAATATATAG
*
534192 ATTTTT-AAAACATTTTGAAAA-CTATATAATATATAG
1 -TTTTTAAAAACATTTTGAAAATATATATAATATATAG
* * **
534228 -TTTTGATAAC-TTTTTTAAA-ATATATAATATAT-G
1 TTTTTAAAAACATTTTGAAAATATATATAATATATAG
* *
534261 GTTTTAAAATA-TTTTTGAAAATATAT
1 TTTTTAAAA-ACATTTTGAAAATATAT
534287 TATTATTATT
Statistics
Matches: 307, Mismatches: 28, Indels: 41
0.82 0.07 0.11
Matches are distributed among these distances:
33 1 0.00
34 36 0.12
35 56 0.18
36 56 0.18
37 48 0.16
38 76 0.25
39 34 0.11
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTTAAAAACATTTTGAAAATATATATAATATATAG
Found at i:535152 original size:14 final size:14
Alignment explanation
Indices: 535133--535166 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
535123 TTTATGATTT
535133 GGGGGGGATTTATA
1 GGGGGGGATTTATA
535147 GGGGGGGATTTATA
1 GGGGGGGATTTATA
535161 GGGGGG
1 GGGGGG
535167 CCACTGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.59, T:0.24
Consensus pattern (14 bp):
GGGGGGGATTTATA
Found at i:535522 original size:5 final size:5
Alignment explanation
Indices: 535514--535637 Score: 51
Period size: 5 Copynumber: 24.0 Consensus size: 5
535504 TTATTTCATT
* * **
535514 TTTTA TTTTA TTTTA --TTA TTTTC TTTTA TTTTTA CTCAA TTTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
* * * *
535562 TATTTA TTGTTT TATTTA TTTTA TTATTA TTATA TTAATA TTTT- TTCTTC
1 T-TTTA TT-TTA T-TTTA TTTTA TT-TTA TTTTA TT-TTA TTTTA TT-TTA
*
535612 TTTT- TTTTCA TATTTT TTTTA TTTTA
1 TTTTA TTTT-A T-TTTA TTTTA TTTTA
535638 CAATCTAACA
Statistics
Matches: 91, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
3 3 0.03
4 10 0.11
5 44 0.48
6 30 0.33
7 4 0.04
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:535524 original size:17 final size:18
Alignment explanation
Indices: 535502--535594 Score: 66
Period size: 17 Copynumber: 5.1 Consensus size: 18
535492 TTTTTTATTT
535502 TTTTATTTCATT-TTTTA
1 TTTTATTTCATTATTTTA
* *
535519 TTTTATTTTATTATTTTC
1 TTTTATTTCATTATTTTA
* *
535537 TTTTATTTTTACTCAATTTTA
1 TTTTA-TTTCA-T-TATTTTA
*
535558 TTTATATTT-ATTGTTTTA
1 TTT-TATTTCATTATTTTA
*
535576 -TTTATTTTATTATTATTA
1 TTTTATTTCATTATT-TTA
535594 T
1 T
535595 ATTAATATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.08
17 18 0.30
18 17 0.28
19 6 0.10
20 2 0.03
21 11 0.18
22 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTTATTTCATTATTTTA
Found at i:535588 original size:12 final size:12
Alignment explanation
Indices: 535495--535598 Score: 62
Period size: 12 Copynumber: 9.0 Consensus size: 12
535485 TTTAACCTTT
*
535495 TTTATTTTTTTA
1 TTTATTTTATTA
535507 TTTCATTTT-TTA
1 TTT-ATTTTATTA
535519 TTTTATTTTATTA
1 -TTTATTTTATTA
*
535532 TTTTCTTTTATT-
1 -TTTATTTTATTA
* * *
535544 TTTA-CTCAAT-
1 TTTATTTTATTA
535554 TTTA-TTTA-TA
1 TTTATTTTATTA
535564 TTTATTGTT-TTA
1 TTTATT-TTATTA
535576 TTTATTTTATTA
1 TTTATTTTATTA
*
535588 -TTATTATATTA
1 TTTATTTTATTA
535599 ATATTTTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
9 1 0.01
10 13 0.17
11 16 0.21
12 24 0.32
13 22 0.29
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:537702 original size:20 final size:20
Alignment explanation
Indices: 537677--537717 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
537667 CCTGCTACAG
*
537677 TGCTACAGTGCATCGATGCA
1 TGCTACAGTGCACCGATGCA
537697 TGCTACAGTGCACCGATGCA
1 TGCTACAGTGCACCGATGCA
537717 T
1 T
537718 AAAAACTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCTACAGTGCACCGATGCA
Found at i:545037 original size:22 final size:22
Alignment explanation
Indices: 545003--545053 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
544993 CTGAGTGGCA
* *
545003 TATGAAGTTTGTCCCAAAGGACC
1 TATGAA-TATGTCCCAAAGAACC
* *
545026 TGTGAATATGTCCCGAAGAACC
1 TATGAATATGTCCCAAAGAACC
545048 TATGAA
1 TATGAA
545054 ACCCTCGATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (22 bp):
TATGAATATGTCCCAAAGAACC
Found at i:556944 original size:27 final size:27
Alignment explanation
Indices: 556888--556946 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
556878 CTAAATTAAT
* * *
556888 TTTTTTCAAGTTCGAGGGTCAAATTGA
1 TTTTTTAAAGTTCAAGGGTCAAATTCA
*
556915 TTTTTTAAAGTTCAAGGG-CACATTTCA
1 TTTTTTAAAGTTCAAGGGTCA-AATTCA
556942 TTTTT
1 TTTTT
556947 AAAATACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (27 bp):
TTTTTTAAAGTTCAAGGGTCAAATTCA
Found at i:559047 original size:14 final size:15
Alignment explanation
Indices: 559028--559056 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
559018 TTGAAACTTT
559028 AAAATC-ATTTTTTC
1 AAAATCTATTTTTTC
559042 AAAATCTATTTTTTC
1 AAAATCTATTTTTTC
559057 TTTCAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAATCTATTTTTTC
Found at i:566335 original size:20 final size:20
Alignment explanation
Indices: 566310--566363 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
566300 TCGGTACCAT
566310 AGGTATCGATACCAATGGGG
1 AGGTATCGATACCAATGGGG
566330 AGGTATCGATACCAATGGGG
1 AGGTATCGATACCAATGGGG
*
566350 ACGTATCGATACCA
1 AGGTATCGATACCA
566364 TTTCTTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (20 bp):
AGGTATCGATACCAATGGGG
Found at i:573488 original size:17 final size:14
Alignment explanation
Indices: 573443--573493 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
573433 AGCATTGTAA
573443 AAAGAAAAT-AATG
1 AAAGAAAATAAATG
573456 AAAGAAAATAAA-G
1 AAAGAAAATAAATG
573469 AAAGAAAGATGAAGATG
1 AAAGAAA-AT-AA-ATG
573486 AAAGAAAA
1 AAAGAAAA
573494 GTATAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
13 17 0.52
14 4 0.12
15 2 0.06
16 2 0.06
17 8 0.24
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (14 bp):
AAAGAAAATAAATG
Found at i:575380 original size:14 final size:14
Alignment explanation
Indices: 575361--575392 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
575351 AATCAGTATA
*
575361 TTTTTATTTTATTT
1 TTTTTATATTATTT
575375 TTTTTATATTATTT
1 TTTTTATATTATTT
575389 TTTT
1 TTTT
575393 AAAAATCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATATTATTT
Found at i:578737 original size:2 final size:2
Alignment explanation
Indices: 578730--578820 Score: 168
Period size: 2 Copynumber: 46.5 Consensus size: 2
578720 TGGGCTTGTA
578730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
578772 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
578812 AT AT AT AT A
1 AT AT AT AT A
578821 ATAATAATAA
Statistics
Matches: 87, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 85 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.