Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008111.1 Hibiscus syriacus cultivar Beakdansim tig00110647_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: 1666726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:446965 original size:27 final size:28
Alignment explanation
Indices: 446935--446988 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
446925 ATTTTCGAAA
446935 ATATATAT-ATCATATAG-TTTTGAAAAC
1 ATATATATAAT-ATATAGTTTTTGAAAAC
446962 ATATATATAATATATAGTTTTTGAAAA
1 ATATATATAATATATAGTTTTTGAAAA
446989 TATGTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (28 bp):
ATATATATAATATATAGTTTTTGAAAAC
Found at i:447012 original size:37 final size:37
Alignment explanation
Indices: 446952--447131 Score: 206
Period size: 37 Copynumber: 4.8 Consensus size: 37
446942 TATCATATAG
446952 TTTTGAAAACATATATATAATATATAGTTTTTGAAAATA-
1 TTTTG-AAA-ATATATATAATATATAG-TTTTGAAAATAT
* *
446991 TGTTGAAAATATATATAATATATAGTTTTGAAAACAT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAATAT
*
447028 TTTTGAGAATATATATAATATATAG-TTTGAAAATCATT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAAT-A-T
* * *
447066 TTTTGAATATATATATAATGTATAGTTTTGAAAGCCT-T
1 TTTTGAAAATATATATAATATATAGTTTTGAAA--ATAT
*
447104 TTTTGAAAATATAAATAATAT-TAGTTTT
1 TTTTGAAAATATATATAATATATAGTTTT
447132 TTATACTATA
Statistics
Matches: 123, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
36 18 0.15
37 48 0.39
38 45 0.37
39 11 0.09
41 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAATAT
Found at i:449210 original size:12 final size:12
Alignment explanation
Indices: 449195--449219 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
449185 ATCTCCCGGA
449195 GAATCTCCAATT
1 GAATCTCCAATT
449207 GAATCTCCAATT
1 GAATCTCCAATT
449219 G
1 G
449220 TTGAGCTCCC
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:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (12 bp):
GAATCTCCAATT
Found at i:449355 original size:18 final size:18
Alignment explanation
Indices: 449332--449372 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
449322 GGGCATTTGA
**
449332 TCCTCTGGTCGTGCTTGT
1 TCCTCTGGTCGAACTTGT
*
449350 TCCTCTGGTGGAACTTGT
1 TCCTCTGGTCGAACTTGT
449368 TCCTC
1 TCCTC
449373 GTACTGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.29, G:0.24, T:0.41
Consensus pattern (18 bp):
TCCTCTGGTCGAACTTGT
Found at i:450981 original size:22 final size:21
Alignment explanation
Indices: 450954--451015 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 21
450944 CAGAACCCCC
**
450954 AGGGGGTATCGATTCCCTTGT
1 AGGGGGTATCGATTCCCTTCA
* * *
450975 GGGGGGGATTCGGTTCCCCTTCA
1 AGGGGGTA-TCGATT-CCCTTCA
450998 AGGGGGTATCGATTCCCT
1 AGGGGGTATCGATTCCCT
451016 CTGCACCAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
21 10 0.32
22 10 0.32
23 11 0.35
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (21 bp):
AGGGGGTATCGATTCCCTTCA
Found at i:457920 original size:5 final size:5
Alignment explanation
Indices: 457910--457965 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
457900 TTATACATTT
* *
457910 TTTTA TTTTA TTTTA TTTTAA TATTT- TCTTCA TCTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A T-TTTA T-TTTA TTTTA TTTTA TTTTA
457957 TTTTA TTTT
1 TTTTA TTTT
457966 TTCTCTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 37 0.86
6 3 0.07
7 3 0.07
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:457929 original size:27 final size:28
Alignment explanation
Indices: 457899--457957 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
457889 AAATTTAACA
* *
457899 TTTATACATTTT-TTTATTTTATTTTAT
1 TTTATACATTTTCTTCATCTTATTTTAT
*
457926 TTTA-ATATTTTCTTCATCTTATTTTAT
1 TTTATACATTTTCTTCATCTTATTTTAT
457953 TTTAT
1 TTTAT
457958 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTATACATTTTCTTCATCTTATTTTAT
Found at i:458421 original size:19 final size:19
Alignment explanation
Indices: 458397--458438 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
458387 ATTGATTGGT
*
458397 GAAGTAGTCAACTATCATG
1 GAAGTAGTAAACTATCATG
*
458416 GAAGTAGTAAACTGTCATG
1 GAAGTAGTAAACTATCATG
458435 GAAG
1 GAAG
458439 GTGATCAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (19 bp):
GAAGTAGTAAACTATCATG
Found at i:460334 original size:30 final size:30
Alignment explanation
Indices: 460298--460357 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
460288 AAGAGAGGCT
*
460298 TGACCAAATGATCAGAGAAAGGCGGGAGAC
1 TGACCAAATGATCAGAGAAAGGCAGGAGAC
460328 TGACCAAATGATCAGAGAAAGGCAGGAGAC
1 TGACCAAATGATCAGAGAAAGGCAGGAGAC
460358 AAGGCATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.32, T:0.10
Consensus pattern (30 bp):
TGACCAAATGATCAGAGAAAGGCAGGAGAC
Found at i:463464 original size:22 final size:21
Alignment explanation
Indices: 463377--463451 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
463367 AAATATGATT
463377 AAATAATTTAT-ATATTATAAA
1 AAAT-ATTTATAATATTATAAA
** *
463398 AGTTATATGA-AATAATTATAAAA
1 AAATAT-TTATAAT-ATTAT-AAA
463421 AAATATTTATAATATTATAAA
1 AAATATTTATAATATTATAAA
463442 AAATATTTAT
1 AAATATTTAT
463452 TTAAATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 2 0.05
21 19 0.44
22 12 0.28
23 10 0.23
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AAATATTTATAATATTATAAA
Found at i:463641 original size:23 final size:23
Alignment explanation
Indices: 463612--463691 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
463602 AGATAATCTA
463612 AAATAATATTATTTAAAATAAAT
1 AAATAATATTATTTAAAATAAAT
* *
463635 AATTAATATTATTTCAAATAAAT
1 AAATAATATTATTTAAAATAAAT
* * *
463658 AAATAATATGATTTTAAA-AATT
1 AAATAATATTATTTAAAATAAAT
463680 AAATAACTATTA
1 AAATAA-TATTA
463692 CTTTGGTTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 9 0.18
23 40 0.82
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (23 bp):
AAATAATATTATTTAAAATAAAT
Found at i:464122 original size:29 final size:27
Alignment explanation
Indices: 464069--464126 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
464059 GTTATAGACT
* *
464069 CATCCTTTAGAAATGAAATCCACCTAC
1 CATCCTTTAAAAAAGAAATCCACCTAC
*
464096 CATCTCTTTAAAAAAGACAATCTACCTAC
1 CATC-CTTTAAAAAAGA-AATCCACCTAC
464125 CA
1 CA
464127 CTATGGTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.15
28 10 0.38
29 12 0.46
ACGTcount: A:0.40, C:0.29, G:0.05, T:0.26
Consensus pattern (27 bp):
CATCCTTTAAAAAAGAAATCCACCTAC
Found at i:464731 original size:22 final size:22
Alignment explanation
Indices: 464706--464768 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
464696 TAGATTGTGC
464706 AGGGGGTACAGATTCCCCCCTG
1 AGGGGGTACAGATTCCCCCCTG
*
464728 AGGGAGTACAGATTCCCCCCTG
1 AGGGGGTACAGATTCCCCCCTG
464750 AGGGGGTATC-GATTCCCCC
1 AGGGGGTA-CAGATTCCCCC
464769 TAAAGAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.32, G:0.30, T:0.19
Consensus pattern (22 bp):
AGGGGGTACAGATTCCCCCCTG
Found at i:466673 original size:16 final size:16
Alignment explanation
Indices: 466652--466703 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
466642 ATGAATGAAA
*
466652 TATTTTAATTAAATTT
1 TATTTTAATTAAAATT
466668 TATTTTAATTAAAATT
1 TATTTTAATTAAAATT
466684 TATTTTTTAATTAAAGATT
1 TA--TTTTAATTAAA-ATT
466703 T
1 T
466704 TCATTTTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 17 0.53
18 11 0.34
19 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTTAATTAAAATT
Found at i:466693 original size:18 final size:17
Alignment explanation
Indices: 466652--466710 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
466642 ATGAATGAAA
466652 TATTTTAATT-AAATTT
1 TATTTTAATTAAAATTT
466668 TATTTTAATTAAAATTT
1 TATTTTAATTAAAATTT
*
466685 ATTTTTTAATTAAAGATTT
1 -TATTTTAATTAAA-ATTT
466704 TCATTTT
1 T-ATTTT
466711 TGTTTACATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 10 0.27
17 6 0.16
18 13 0.35
19 8 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTTTAATTAAAATTT
Found at i:466731 original size:17 final size:17
Alignment explanation
Indices: 466709--466741 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
466699 GATTTTCATT
466709 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
466726 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
466742 TCAAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:473510 original size:21 final size:23
Alignment explanation
Indices: 473484--473534 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
473474 AGGGTATCGA
473484 TCCCCCCATG-A-GGAAACCGAT
1 TCCCCCCATGAAGGGAAACCGAT
** *
473505 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGAAACCGAT
473528 TCCCCCC
1 TCCCCCC
473535 CCCCCACAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.22, C:0.41, G:0.20, T:0.18
Consensus pattern (23 bp):
TCCCCCCATGAAGGGAAACCGAT
Found at i:483473 original size:13 final size:14
Alignment explanation
Indices: 483455--483486 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
483445 TAAATAATTC
483455 TAAAAATATTA-TT
1 TAAAAATATTATTT
483468 TAAAAATATTATTT
1 TAAAAATATTATTT
483482 TAAAA
1 TAAAA
483487 CTAAAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAAATATTATTT
Found at i:484780 original size:3 final size:3
Alignment explanation
Indices: 484770--484815 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
484760 GTATTATTTG
* *
484770 TAA T-A TAA TAA TAT TAA T-A TAA TAA TAA TAA TATA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
484814 TA
1 TA
484816 CGGTACGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:484787 original size:14 final size:14
Alignment explanation
Indices: 484770--484815 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
484760 GTATTATTTG
*
484770 TAATATAATAATAT
1 TAATATAATAATAA
484784 TAATATAATAATAA
1 TAATATAATAATAA
484798 TAATAT-ATAATAA
1 TAATATAATAATAA
*
484811 AAATA
1 TAATA
484816 CGGTACGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:486456 original size:23 final size:22
Alignment explanation
Indices: 486430--486473 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
486420 CAAAATATTA
486430 TGTACTGTAACTATGTATTTTTT
1 TGTACTGTAACTATGT-TTTTTT
486453 TGTACTGTAACTATGTTTTTT
1 TGTACTGTAACTATGTTTTTT
486474 AACTTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (22 bp):
TGTACTGTAACTATGTTTTTTT
Found at i:487024 original size:18 final size:16
Alignment explanation
Indices: 486984--487037 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
486974 ATGAATGAAA
486984 TTTTTTTAATT-AAAT
1 TTTTTTTAATTAAAAT
486999 TTTATTTTAATTAAAAGT
1 TTT-TTTTAATTAAAA-T
487017 TATTTTTTAATTAAAGAT
1 T-TTTTTTAATTAAA-AT
487035 TTT
1 TTT
487038 CATTTTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
17 5 0.15
18 15 0.44
19 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (16 bp):
TTTTTTTAATTAAAAT
Found at i:487064 original size:17 final size:17
Alignment explanation
Indices: 487042--487074 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
487032 GATTTTCATT
487042 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
487059 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
487075 TCAAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:490091 original size:21 final size:21
Alignment explanation
Indices: 490065--490105 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
490055 CGATAAAAAA
* *
490065 TACTTAAAATATTATTATTTC
1 TACTTAAAACATTAATATTTC
490086 TACTTAAAACATTAATATTT
1 TACTTAAAACATTAATATTT
490106 TTTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
TACTTAAAACATTAATATTTC
Found at i:491737 original size:27 final size:27
Alignment explanation
Indices: 491681--491738 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
491671 TAAATTAAGA
* *
491681 TCTAATAAATAATATTAGATTCTTTAT
1 TCTAATAAATAATATTAGATACTATAT
* *
491708 TCTAATTAATAATAGTTTGATACTAT-T
1 TCTAATAAATAATA-TTAGATACTATAT
491735 TCTA
1 TCTA
491739 TAATTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (27 bp):
TCTAATAAATAATATTAGATACTATAT
Found at i:499920 original size:20 final size:20
Alignment explanation
Indices: 499897--499953 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
499887 TGTTGGCCCT
499897 TTAGTATCGATACTGACCCC
1 TTAGTATCGATACTGACCCC
* * *
499917 TTAGTATCAATACTCACCTC
1 TTAGTATCGATACTGACCCC
*
499937 TTGGTATCGATACTGAC
1 TTAGTATCGATACTGAC
499954 TGAATGAGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (20 bp):
TTAGTATCGATACTGACCCC
Found at i:513544 original size:20 final size:20
Alignment explanation
Indices: 513461--513547 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
513451 GTACATTTAC
* * *
513461 TATCAATATTGTTCATACAG
1 TATCGATATTATTCTTACAG
* *
513481 TATCGATACTATTCTTTATTAG
1 TATCGATATTATTC-TTA-CAG
*
513503 TATCGATATTATTCGT-CAAG
1 TATCGATATTATTCTTAC-AG
513523 TATCGATATTATTCTTACAG
1 TATCGATATTATTCTTACAG
513543 TATCG
1 TATCG
513548 TTAGTAGTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 35 0.65
21 4 0.07
22 15 0.28
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
TATCGATATTATTCTTACAG
Found at i:514440 original size:12 final size:12
Alignment explanation
Indices: 514423--514452 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
514413 TCTCCTACTT
514423 CAAATCCACCTC
1 CAAATCCACCTC
514435 CAAATCCACCTC
1 CAAATCCACCTC
514447 CAAATC
1 CAAATC
514453 ATATTCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.17
Consensus pattern (12 bp):
CAAATCCACCTC
Found at i:517637 original size:33 final size:32
Alignment explanation
Indices: 517561--517640 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 32
517551 CAACGCGTTG
517561 CCAGAAAACCAGCC-CGACCACCAAGCATATTT
1 CCAGAAAACCA-CCTCGACCACCAAGCATATTT
* * *
517593 CTTTA-AAAACCACCTCGACTACCAAGCGTATTT
1 C--CAGAAAACCACCTCGACCACCAAGCATATTT
517626 CCAGAATAACCACCT
1 CCAGAA-AACCACCT
517641 GTTCTAGAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
31 1 0.03
32 5 0.13
33 32 0.82
34 1 0.03
ACGTcount: A:0.36, C:0.35, G:0.10, T:0.19
Consensus pattern (32 bp):
CCAGAAAACCACCTCGACCACCAAGCATATTT
Found at i:518769 original size:19 final size:19
Alignment explanation
Indices: 518745--518784 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
518735 CTAACATATA
* *
518745 ATTTTAAATGTATTTTTTT
1 ATTTTAAATATATCTTTTT
518764 ATTTTAAATATATCTTTTT
1 ATTTTAAATATATCTTTTT
518783 AT
1 AT
518785 ACTATGTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTAAATATATCTTTTT
Found at i:520338 original size:3 final size:3
Alignment explanation
Indices: 520325--520374 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
520315 ATTTTTATAT
*
520325 TAA TAA T-A TAA TAAA TAA TAA TAA TAA TAA TAA -AA CAAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
520370 TAA TA
1 TAA TA
520375 TTGAAATGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
2 4 0.10
3 33 0.79
4 5 0.12
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:520349 original size:21 final size:20
Alignment explanation
Indices: 520325--520375 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
520315 ATTTTTATAT
520325 TAATAATATAATAA-ATAATAA
1 TAATAATATAA-AACA-AATAA
520346 TAATAATAATAAAACAAATAA
1 TAATAAT-ATAAAACAAATAA
520367 TAATAATAT
1 TAATAATAT
520376 TGAAATGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.07
21 21 0.75
22 5 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TAATAATATAAAACAAATAA
Found at i:520352 original size:24 final size:24
Alignment explanation
Indices: 520325--520374 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
520315 ATTTTTATAT
* *
520325 TAATAATATAATAAATAATAATAA
1 TAATAATAAAACAAATAATAATAA
520349 TAATAATAAAACAAATAATAATAA
1 TAATAATAAAACAAATAATAATAA
520373 TA
1 TA
520375 TTGAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
TAATAATAAAACAAATAATAATAA
Found at i:526012 original size:11 final size:11
Alignment explanation
Indices: 525983--526012 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
525973 ATATATTCTT
525983 ATTTAAAAATA
1 ATTTAAAAATA
525994 ATTATAAAAATA
1 ATT-TAAAAATA
526006 ATTTAAA
1 ATTTAAA
526013 TAAAAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:527629 original size:20 final size:19
Alignment explanation
Indices: 527590--527629 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
527580 ATTAATAATC
*
527590 TTAAAATTCAATGCTATAA
1 TTAAAATTCAATGATATAA
*
527609 TTAAAATTTAGATGATATAA
1 TTAAAATTCA-ATGATATAA
527629 T
1 T
527630 AAGTAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (19 bp):
TTAAAATTCAATGATATAA
Found at i:528630 original size:31 final size:32
Alignment explanation
Indices: 528595--528659 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
528585 AAAGATAAAT
* *
528595 TTATAATTTGAATCTTAAA-TATTTTTTATGA
1 TTATAATTTGAATATTAAATTATTTTTAATGA
528626 TTATAATTTGAATATTAAATTATTTTTAATGA
1 TTATAATTTGAATATTAAATTATTTTTAATGA
528658 TT
1 TT
528660 TCAGTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (32 bp):
TTATAATTTGAATATTAAATTATTTTTAATGA
Found at i:529512 original size:80 final size:80
Alignment explanation
Indices: 529352--529502 Score: 257
Period size: 80 Copynumber: 1.9 Consensus size: 80
529342 ATTGCATTAA
* * *
529352 ATGAAAATCCAAGGAAGCAAATCATATTCAATTAGTGACCAAAATGGAAGAAAATAAAGTAGGGT
1 ATGAAAATCCAAGGAAGCAAATCATATACAAGTAGTGACCAAAATGGAAGAAAATAAAGTAGAGT
*
529417 TCTAGCACCACGAAT
66 TCCAGCACCACGAAT
*
529432 ATGAAAATTCAAGGAAGCAAATCATATACAAGTAGTGACCAAAATGGAAGAAAATAAAGTAGAGT
1 ATGAAAATCCAAGGAAGCAAATCATATACAAGTAGTGACCAAAATGGAAGAAAATAAAGTAGAGT
529497 TCCAGC
66 TCCAGC
529503 GTCGCGAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (80 bp):
ATGAAAATCCAAGGAAGCAAATCATATACAAGTAGTGACCAAAATGGAAGAAAATAAAGTAGAGT
TCCAGCACCACGAAT
Found at i:535851 original size:16 final size:16
Alignment explanation
Indices: 535819--535862 Score: 79
Period size: 16 Copynumber: 2.7 Consensus size: 16
535809 GTATTATTGT
535819 AATTATATATAAGGTAA
1 AATTATATAT-AGGTAA
535836 AATTATATATAGGTAA
1 AATTATATATAGGTAA
535852 AATTATATATA
1 AATTATATATA
535863 TTTTCGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (16 bp):
AATTATATATAGGTAA
Found at i:535993 original size:26 final size:26
Alignment explanation
Indices: 535964--536025 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
535954 AGTTTCACCC
535964 AACCCGACCCTAATATATGAATTAGA
1 AACCCGACCCTAATATATGAATTAGA
* *
535990 AACCCGACCTTAATATATGAGTTAGA
1 AACCCGACCCTAATATATGAATTAGA
536016 AACCCGACCC
1 AACCCGACCC
536026 GAAATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (26 bp):
AACCCGACCCTAATATATGAATTAGA
Found at i:537463 original size:16 final size:19
Alignment explanation
Indices: 537442--537484 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
537432 AACATTTCCA
537442 GTAATC-ATATTC-C-CTG
1 GTAATCTATATTCTCACTG
537458 GTAATCTTATATTCTCACTG
1 GTAATC-TATATTCTCACTG
537478 GTAATCT
1 GTAATCT
537485 TACATTCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.26
18 6 0.26
19 2 0.09
20 9 0.39
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (19 bp):
GTAATCTATATTCTCACTG
Found at i:537471 original size:18 final size:19
Alignment explanation
Indices: 537448--537492 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
537438 TCCAGTAATC
537448 ATATTCC-CTGGTAATCTT
1 ATATTCCACTGGTAATCTT
537466 ATATTCTCACTGGTAATCTT
1 ATATTC-CACTGGTAATCTT
*
537486 ACATTCC
1 ATATTCC
537493 GTGAACCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 16 0.67
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (19 bp):
ATATTCCACTGGTAATCTT
Found at i:543546 original size:197 final size:197
Alignment explanation
Indices: 543238--543614 Score: 610
Period size: 197 Copynumber: 1.9 Consensus size: 197
543228 TGTCAAAACT
* *
543238 GGTAAAGAGTTACCGGAATTCTTGAAATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTA
1 GGTAAAGAGCTACCGGAATGCTTGAAATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTA
* * *
543303 TTGGTACTTTAGGAATTTAAAAGAATTGCAATAATAGCGGCTATAAAGTATCGATACCTTACACA
66 TCGATACTTTAGGAATTTAAAAAAATTGCAATAATAGCGGCTATAAAGTATCGATACCTTACACA
*
543368 AATGTATCGATACATGACAATATAACAGGTTGAAATTTGACAAAACCAGTTTCAATTTGACAAAA
131 AATGTATCGATACATGACAATATAACAAGTTGAAATTTGACAAAACCAGTTTCAATTTGACAAAA
543433 GC
196 GC
* * **
543435 GGTAAAGAGCTACTGGAATGGTTGAAATTTGTATCGATATTTTTATAAGTATATGTACCAAAGTA
1 GGTAAAGAGCTACCGGAATGCTTGAAATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTA
* * * *
543500 TCGATACTTTATGAATTTAAAAAAATTGTAATAATAGCGTCTATAAAGTATCGATACCTTAGACA
66 TCGATACTTTAGGAATTTAAAAAAATTGCAATAATAGCGGCTATAAAGTATCGATACCTTACACA
* *
543565 CATGTATCGATACATGACAATATAACAAGTTGGAATTTGACAAAACCAGT
131 AATGTATCGATACATGACAATATAACAAGTTGAAATTTGACAAAACCAGT
543615 AAAGCGATAC
Statistics
Matches: 164, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
197 164 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (197 bp):
GGTAAAGAGCTACCGGAATGCTTGAAATTTGTATCGATACGTTTATAAGTATATGTACCAAAGTA
TCGATACTTTAGGAATTTAAAAAAATTGCAATAATAGCGGCTATAAAGTATCGATACCTTACACA
AATGTATCGATACATGACAATATAACAAGTTGAAATTTGACAAAACCAGTTTCAATTTGACAAAA
GC
Found at i:547896 original size:30 final size:29
Alignment explanation
Indices: 547862--547930 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
547852 AAATTACAAT
*
547862 TTTAGTCC-CTAAACTTTTCAAAATTTATA
1 TTTAGTCCACTAAAC-TTTCAAAACTTATA
547891 CTTTAG-CCACTAAACTTTCAAAACTTATA
1 -TTTAGTCCACTAAACTTTCAAAACTTATA
547920 TTTAGT-CACTA
1 TTTAGTCCACTA
547931 GACAAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 10 0.28
29 15 0.42
30 11 0.31
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (29 bp):
TTTAGTCCACTAAACTTTCAAAACTTATA
Found at i:548837 original size:225 final size:226
Alignment explanation
Indices: 548256--548863 Score: 848
Period size: 226 Copynumber: 2.7 Consensus size: 226
548246 TGTACACGGG
* *
548256 AATATATTGATAATATTGAAAACAAATCAAGTAATTAGCCTATTTTGTTATCGTCGAATTTCTAA
1 AATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGAATTTCTAA
* * *
548321 GGCCTCATTAGCTTTAAACAAACACTACCTATTACATTAAATAAGTGTTACTTGTTATGTTATTA
66 AGCCTCATCAGCTTTAAACAAACACTACCTATTATATTAAATAAGTGTTACTTGTTATGTTATTA
* * * * * *
548386 TGGTTGATAATGTTTCCAGTAATTAACTTATTTTGTTATCGTCGGATTTTTATGGCTCCATCAGC
131 TGGTTGATAATGTTTCTAGTAATTAACTTATTTTGTTATCGTCAGATTTCTAAGACTCCAACAGC
*
548451 TTAAACTTTGGTAACATTTTTTGTGCTACCT
196 TTAAACTTTGGTAACATTTTTGGTGCTACCT
*
548482 AATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTTGAATTTCTAA
1 AATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGAATTTCTAA
* * * * *
548547 AGCCCCATCATCTTTAAACAAACGCTACTTATTATATTAAATAAGTGTTAATTGTTATGTTATTA
66 AGCCTCATCAGCTTTAAACAAACACTACCTATTATATTAAATAAGTGTTACTTGTTATGTTATTA
*
548612 TGGTTGATAATGTTTCTAGTAATTAACTTATTTTGTTATCGTCAGATTTCTAAGACTTCAACAGC
131 TGGTTGATAATGTTTCTAGTAATTAACTTATTTTGTTATCGTCAGATTTCTAAGACTCCAACAGC
*
548677 TTAAACTTTGGTAGCA-TTTTGGTGCTACCT
196 TTAAACTTTGGTAACATTTTTGGTGCTACCT
* * * * * *
548707 AATATGTT-ACTAATATTGATAATAAATTAAGTAATTAACATATTTTGTTAACGTC-AGATTTTT
1 AATATATTGA-TAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGA-ATTTCT
* ** * *
548770 AAAGCCTCATCAGCTTTAAA-AAGACACTACCTATTATA-TAACATAAGCGCCACCTGTTATATT
64 AAAGCCTCATCAGCTTTAAACAA-ACACTACCTATTATATTAA-ATAAGTGTTACTTGTTATGTT
* *
548833 ATTATGATTGATAATATTTCTAGTAATTAAC
127 ATTATGGTTGATAATGTTTCTAGTAATTAAC
548864 CGGTTATGTT
Statistics
Matches: 339, Mismatches: 39, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
224 7 0.02
225 140 0.41
226 192 0.57
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (226 bp):
AATATATTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGAATTTCTAA
AGCCTCATCAGCTTTAAACAAACACTACCTATTATATTAAATAAGTGTTACTTGTTATGTTATTA
TGGTTGATAATGTTTCTAGTAATTAACTTATTTTGTTATCGTCAGATTTCTAAGACTCCAACAGC
TTAAACTTTGGTAACATTTTTGGTGCTACCT
Found at i:549374 original size:20 final size:21
Alignment explanation
Indices: 549349--549392 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
549339 CCGGAAATGT
* *
549349 TAAAAA-ATTAATGTTTTAGA
1 TAAAAATAATAATATTTTAGA
549369 TAAAAATAATAATATTTTAGA
1 TAAAAATAATAATATTTTAGA
549390 TAA
1 TAA
549393 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGA
Found at i:549671 original size:23 final size:23
Alignment explanation
Indices: 549624--549673 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
549614 AATAACATAT
**
549624 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
549647 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
549670 TAGG
1 TAGG
549674 CATTTAACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:552884 original size:201 final size:198
Alignment explanation
Indices: 552403--552947 Score: 693
Period size: 201 Copynumber: 2.7 Consensus size: 198
552393 GCGTAATTTT
* * * *
552403 AAAAAGTGTCGACACATTATGTT-GACCTATTTTCT-ATTTACACCGGTAAATTTCAACCGGTTA
1 AAAAAGTGTCGATACATTAT-TTAGACCTATTTTCTCA-TAAAACCGGTAAATTTAAACCGGTTA
* **
552466 CATTGTAAATTGACCTATTACATTATAATTTTCGGTCTCGATGTATTTGGGGTTAATACTTTTTA
64 CATTGTAAATTGACCTATTACATTATAATTTTCGGTCTCAATGTATTTGGGGTCGATAC-TTTTA
* * * * * * *
552531 TAAATGTATCGAAACTTTATGCGTGGACATCGGTTGGCATTAATTATGGACATAAGTATCGACAC
128 TAAATGTATCGAAACTTCAAGCGTGCACATAGGTTGGAATTAATTATGGAAAAAAGTATCGACAC
*
552596 AAATGT
193 AAATGA
* * *
552602 AAAAAGTATCGATACATTATGTAGACCTATTTGCTCATAAAACCGGTAAATTTAAACCGGTTACA
1 AAAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACA
*
552667 TTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCAATGTATTTGGGGTCGATACTTTTAATA
66 TTGTAAATTGACCTATTACATTATAATTTTCGGTCTCAATGTATTTGGGGTCGATACTTTT-ATA
* * * *
552732 AATGTATCGACACTTCAAGCGTGCACATAGTTTGGGAATTTATTATGGATAAAAAGTATTGACAC
130 AATGTATCGAAACTTCAAGCGTGCACATAGGTT-GGAATTAATTATGGA-AAAAAGTATCGACAC
552797 AAAT-A
193 AAATGA
* *
552802 AATAAAGTGTCGATACATTATTTAGACATATTTTCTCATAAAACCGGTAAATTTAAACCAGTTAC
1 AA-AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTAC
* * * * * * *
552867 ATTGTTAATTTACCTATTACATTATAATTAT-GAGTTTCAATGTTTTTGGGATCGACACTTGTTA
65 ATTGTAAATTGACCTATTACATTATAATTTTCG-GTCTCAATGTATTTGGGGTCGATACTT-TTA
552931 TAAATGTATCGAAACTT
128 TAAATGTATCGAAACTT
552948 TGTTGTGCAC
Statistics
Matches: 301, Mismatches: 37, Indels: 14
0.86 0.11 0.04
Matches are distributed among these distances:
198 5 0.02
199 137 0.46
200 17 0.06
201 140 0.47
202 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (198 bp):
AAAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACCGGTAAATTTAAACCGGTTACA
TTGTAAATTGACCTATTACATTATAATTTTCGGTCTCAATGTATTTGGGGTCGATACTTTTATAA
ATGTATCGAAACTTCAAGCGTGCACATAGGTTGGAATTAATTATGGAAAAAAGTATCGACACAAA
TGA
Found at i:553774 original size:200 final size:200
Alignment explanation
Indices: 552808--553765 Score: 1370
Period size: 200 Copynumber: 4.8 Consensus size: 200
552798 AATAAATAAA
* * * * * * *
552808 GTGTCGATACATTATTTAGACATATTTTCTCATAAAACCGGTAAATTTAAACCAGTTACATTGTT
1 GTGTCGATACTTTATGTATACATGTTTTCTCAT-AAACCGGTATATTTAGACCGGTTACATTGTT
* *
552873 AATTTACCTATTACATTATAATTATGAGTTTCAATGTTTTTGGGATCGACACTTGTTATAAATGT
65 AATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATGT
* * *
552938 ATCGAAACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATTGATACTTATT
130 ATCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTATT
*
553003 GGATTT
195 GTATTT
* * * *
553009 GTGTCGATACTTTATGTGTACCTGTTTTCTCATAAATCGGTATATTTAGACCGATTACATTGTTA
1 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* *
553074 ATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTCA-GATCGAAACTTGTTATAAATGT
66 ATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTT-AGGATCGACACTTGTTATAAATGT
*
553138 ATCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTT
130 ATCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTATT
553203 -TCATTT
195 GT-ATTT
* * * *
553209 GTGTCGATACTTTATATATACCTATTTTCTCATAAACCGATATATTTAGACCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* *
553274 ATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTA
66 ATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATGTA
*
553339 TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTATTG
131 TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTATTG
*
553404 CATTT
196 TATTT
* * * *
553409 GTGTCGATACTTTATGTTTACATGTTTTCTAAAAAACCGGTATATTTAGGCCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* * *
553474 TTTTACCTATTACATTAT-ATCTATGTGTTTCGATGTTTTTAGTATCGACACTTGTTATAAATGT
66 ATTTACCTATTACATTATAAT-TATGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATGT
* * * *
553538 ATCGAAACGTTT-TAGTGCACTTGGTTTATAAAATACACACTGGACAAAAAGTATCGACACTTAT
130 ATCGACAC-TTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTAT
553602 TGTATTT
194 TGTATTT
* * *
553609 GTGTCGATACTTTATGTATACATGTTTTCTCA-AAAGTCGATATATTTAGGCCGGTTACATTGTT
1 GTGTCGATACTTTATGTATACATGTTTTCTCATAAA-CCGGTATATTTAGACCGGTTACATTGTT
* * * * *
553673 ATTTTACCTATTACATTAT-ATCTATGTGTTTCGATATTTTTAGTATCGACACTTGCTATAAATG
65 AATTTACCTATTACATTATAAT-TATGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATG
*
553737 TATCGACACTTTTTTCGTGCACTTGGTTT
129 TATCGACACTTTGTT-GTGCACTTGGTTT
553766 GGAAATACAT
Statistics
Matches: 689, Mismatches: 59, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
199 8 0.01
200 638 0.93
201 43 0.06
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (200 bp):
GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
ATTTACCTATTACATTATAATTATGAGTTTCGATGTTTTTAGGATCGACACTTGTTATAAATGTA
TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTATTG
TATTT
Found at i:554016 original size:24 final size:24
Alignment explanation
Indices: 553979--554025 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
553969 ATTTACATTT
553979 AAATTCAAACTCAAACTCAAATTG
1 AAATTCAAACTCAAACTCAAATTG
* * *
554003 AAATTTAAATTCAAACTCTAATT
1 AAATTCAAACTCAAACTCAAATT
554026 ATAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAACTCAAATTG
Found at i:556636 original size:30 final size:30
Alignment explanation
Indices: 556586--556671 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
556576 CGATGTTTGA
*
556586 GAAAGAGGTTGTGATTGAGAAGAGCTGGGTTG
1 GAAAGAGG-TG-GGTTGAGAAGAGCTGGGTTG
* *
556618 GAAAGAGGTGGGTTGAGAACAGTTGGGTTG
1 GAAAGAGGTGGGTTGAGAAGAGCTGGGTTG
*
556648 GGAAGAGGTGGGTTGAGAAGAGCT
1 GAAAGAGGTGGGTTGAGAAGAGCT
556672 TTGAGAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 38 0.79
31 2 0.04
32 8 0.17
ACGTcount: A:0.28, C:0.03, G:0.47, T:0.22
Consensus pattern (30 bp):
GAAAGAGGTGGGTTGAGAAGAGCTGGGTTG
Found at i:556667 original size:15 final size:15
Alignment explanation
Indices: 556600--556669 Score: 88
Period size: 15 Copynumber: 4.7 Consensus size: 15
556590 GAGGTTGTGA
*
556600 TTGAGAAGAGCTGGG
1 TTGAGAAGAGGTGGG
556615 TTG-GAAAGAGGTGGG
1 TTGAG-AAGAGGTGGG
* *
556630 TTGAGAACAGTTGGG
1 TTGAGAAGAGGTGGG
*
556645 TTGGGAAGAGGTGGG
1 TTGAGAAGAGGTGGG
556660 TTGAGAAGAG
1 TTGAGAAGAG
556670 CTTTGAGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
14 1 0.02
15 44 0.96
16 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.49, T:0.21
Consensus pattern (15 bp):
TTGAGAAGAGGTGGG
Found at i:557471 original size:199 final size:199
Alignment explanation
Indices: 557018--558515 Score: 2167
Period size: 199 Copynumber: 7.5 Consensus size: 199
557008 TTTTCAAATT
* * * * *
557018 AAACAGGTATTTTTATACCAGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * *
557083 TGTTTTTGGGATCGACACTTGTTATAAATATATCGAAACTTTGTT-GTGCACTTGGTTTTTAAAA
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTT-TTAGTGCACTTGG-TTTTGAAA
* ** * * *
557147 TACACTCTGGA-CAATAAGTATCGACACTTGTTGGATTTGTGTCGATACTTTATGTATACCTATT
129 TACATTCTGGACCAA-AAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTT
*
557211 TTCTCAT
193 TTCTCAA
** *
557218 AAACCAATATATTTAGACTGG-TAACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCG
1 AAACCGGTATATTTAGACCGGTTAA-ATTGTTAATTTACCTATTACATTATAATTATGGGTTTCG
*
557282 ATGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTCGAAAT
65 ATGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAAT
* *
557347 ACATTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACTTGTTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
557412 CTCAA
195 CTCAA
* * * * *
557417 AAACTGGTATATTTAAACCAGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCAA
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * ** **
557482 TATTTTTGGGATCGACACTTGTTATAAATATATCGACACTTTTCCGTGCACTTGGTTAAGAAATA
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* *
557547 CATTCTGGACCAAAAATATCGACACTTGTTTTAGTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
557612 TCAA
196 TCAA
* * * * *
557616 AAACCGGTATATTTATACCGGTTACATTGCTAATTTACCTATTACATTATAATTATAGGTTTCAA
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
557681 TATTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
*
557746 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTTGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
557811 TCAA
196 TCAA
* *
557815 AAACCGGTATATTTAGACCAGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * ** **
557880 TGTTTTTGAGATCGACACTTGTTATAAATGTATTGACACTTTTCCGTGCACTTGGTTAAGAAATA
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * * * *
557945 CATTCTGGACCAAAAGAATCGACACTTTTTTTAGTTATGTCGATACTTTTTGTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
558010 T-ATA
196 TCA-A
* *
558014 AAACCAGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* **
558079 TGTTTTTGGGATCTACACTTCTTATAAATGTATATACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* *
558144 CATTCTGGACTAAAAGTGTCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
558209 TCAA
196 TCAA
* * * * *
558213 AAACTGATATATTTAGACCGGTTAAATTGTTAATTTACTTATTACATCATAATTATGGGTTTCAA
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * * *
558278 TGTTTTTGGGATCGACACATGTTATAAATATATCGACACTTTTTAGTGCACTTGGTTTTAAAATA
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * * * * *
558343 CATTATAGACCAAAAGTATCGACACTTGTTTTAGTTGTGTCGATATTTTTTGTACGCATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
558408 TCAA
196 TCAA
* * *
558412 AAATCGGTATATTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGC
1 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* *
558477 TATTTTTGGGATCGACACTTCTTATAAATGTATTGACAC
66 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACAC
558516 ATAAGTTTAC
Statistics
Matches: 1159, Mismatches: 133, Indels: 13
0.89 0.10 0.01
Matches are distributed among these distances:
198 1 0.00
199 1048 0.90
200 110 0.09
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
TCAA
Found at i:558910 original size:19 final size:19
Alignment explanation
Indices: 558886--558935 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
558876 TTACATTCAC
*
558886 ATACAAAATTATAAATCAT
1 ATACAAAATTAAAAATCAT
*
558905 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCAT
558924 ATACAAAATTAA
1 ATACAAAATTAA
558936 CCCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCAT
Found at i:560853 original size:9 final size:9
Alignment explanation
Indices: 560836--560876 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
560826 ATTCTTCCTT
*
560836 CTCCACTGC
1 CTCCTCTGC
560845 CTCCTCTGC
1 CTCCTCTGC
*
560854 TTCCTCTGC
1 CTCCTCTGC
*
560863 CTCCTCTAC
1 CTCCTCTGC
560872 CTCCT
1 CTCCT
560877 TGACAATAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.05, C:0.54, G:0.07, T:0.34
Consensus pattern (9 bp):
CTCCTCTGC
Found at i:561135 original size:22 final size:21
Alignment explanation
Indices: 561107--561162 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
561097 AACCTGCATT
*
561107 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
561129 TATAATAACTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
561153 TATAA-AAAAC
1 TATAATAAAAC
561163 AAAAACATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 2 0.07
21 1 0.03
22 8 0.27
23 2 0.07
24 16 0.53
25 1 0.03
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:562448 original size:19 final size:19
Alignment explanation
Indices: 562424--562485 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
562414 TACAATCTAA
*
562424 AATATCATTTTCTACCTAT
1 AATATCATTTTTTACCTAT
562443 AATATCATTTTTTACCTAT
1 AATATCATTTTTTACCTAT
*
562462 AATATCATTTTTTACATAT
1 AATATCATTTTTTACCTAT
562481 AATAT
1 AATAT
562486 TAAATAAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATCATTTTTTACCTAT
Found at i:563180 original size:182 final size:181
Alignment explanation
Indices: 562868--563529 Score: 785
Period size: 182 Copynumber: 3.6 Consensus size: 181
562858 TACGTGTACT
* * * *
562868 TATTAAAATATCGACGCTTTCAACATATCCGATAGCGCTTTACCGATTTTGTCATTTTGAGACTG
1 TATTAAATTATCGACACTTTCAACATATCCGATATCGCTTTACCGATTTTGTCATTTTGAAAC-G
* * * *
562933 TTTTTATTATATTTTTACCTGTTATATTGTTATAGATCGATACATTTTTTAAAAGTATCGACACT
65 ATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
562998 TTATAGGCGTTATAACTTCTTCTCTTTTAAATTTTAAAAGTGTCGATACTTA
130 TTATAGACGTTATAACTTCTTCTCTTTTAAATTTTAAAAGTGTCGATACTTA
* ** *
563050 TATTAAATTATCGTCACTTTCAACATATCCGATATCTTTTTACTG-TTTTGTCATTTTTGAAACA
1 TATTAAATTATCGACACTTTCAACATATCCGATATCGCTTTACCGATTTTGTCA-TTTTGAAAC-
* * *
563114 TATTTTATCATATTTTTATCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATTGACAC
64 GATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
* ** * *
563179 TTTATAGACGTTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTTGATACATA
129 TTTATAGACGTTATAACTTCTTCTCTTTTAAATTTTAAAAGTGTCGATACTTA
* * * *** *
563232 TATTAAAGTATCGACACTTTCGACATAT-CTATATTTATTTACCTG-TTTTGTCATTTTGAGATC
1 TATTAAATTATCGACACTTTCAACATATCCGATATCGCTTTACC-GATTTTGTCATTTTGA-AAC
* * * ** * *
563295 GATTTTGTTATATTTTTAACTGTTATATTGTTATGGATCGATACATTTTCATAAATTGTCGACAC
64 GATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
563360 TTTAT-GAACGTTATAACTTCTTCTCTTTTAAA-TTTAGAAAGTGTCGATACTTA
129 TTTATAG-ACGTTATAACTTCTTCTCTTTTAAATTTTA-AAAGTGTCGATACTTA
* * * * * * *
563413 TATTAAATTATCGACACTTTTAATATATCTGATAACGCTTTACCGATTTTGTTATTTTTAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGATATCGCTTTACCGATTTTGTCATTTTGA-AACG
* * * ** *
563478 ATTTTGTCATATTTTTACCTGTAACATTACTATGGAGCGATACATTTTTTTA
65 ATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTA
563530 TTTGTATCGA
Statistics
Matches: 407, Mismatches: 66, Indels: 14
0.84 0.14 0.03
Matches are distributed among these distances:
180 3 0.01
181 149 0.37
182 255 0.63
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (181 bp):
TATTAAATTATCGACACTTTCAACATATCCGATATCGCTTTACCGATTTTGTCATTTTGAAACGA
TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTT
TATAGACGTTATAACTTCTTCTCTTTTAAATTTTAAAAGTGTCGATACTTA
Found at i:563479 original size:20 final size:21
Alignment explanation
Indices: 563454--563494 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
563444 ATAACGCTTT
563454 ACCGATTTTGT-TATTTTTAG
1 ACCGATTTTGTATATTTTTAG
563474 ACCGATTTTGTCATATTTTTA
1 ACCGATTTTGT-ATATTTTTA
563495 CCTGTAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.54
Consensus pattern (21 bp):
ACCGATTTTGTATATTTTTAG
Found at i:567427 original size:12 final size:12
Alignment explanation
Indices: 567410--567436 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
567400 TTTCATTTTC
567410 TTTATTATTATT
1 TTTATTATTATT
567422 TTTATTATTATT
1 TTTATTATTATT
567434 TTT
1 TTT
567437 CCCTTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:568581 original size:22 final size:22
Alignment explanation
Indices: 568555--568601 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
568545 TTTTCCTTTA
* * *
568555 ATTTTTATTT-TCTTTTACTTC
1 ATTTTTTTTTATCATTTACATC
568576 ATTTTTTTTTATCATTTACATC
1 ATTTTTTTTTATCATTTACATC
568598 ATTT
1 ATTT
568602 AAAAGAGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (22 bp):
ATTTTTTTTTATCATTTACATC
Found at i:569225 original size:23 final size:23
Alignment explanation
Indices: 569199--569254 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
569189 TAAAATGTTT
* *
569199 TTTTGTCTCTTAAGAAATAACAC
1 TTTTGTCCCCTAAGAAATAACAC
*
569222 TTTTGTCCCCTAAGAAATAACAT
1 TTTTGTCCCCTAAGAAATAACAC
569245 TTTTGTCCCC
1 TTTTGTCCCC
569255 AATAAGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (23 bp):
TTTTGTCCCCTAAGAAATAACAC
Found at i:571587 original size:43 final size:43
Alignment explanation
Indices: 571539--571621 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
571529 CGAAGGGGCC
*
571539 ATCCACGATTTCAACTCCACAACGGAGGATATTGTGCCCACAA
1 ATCCACGATTTCAACTCCACAACGAAGGATATTGTGCCCACAA
* ***
571582 ATCCACGATTTCAACTTCACGGTGAAGGATATTGTGCCCA
1 ATCCACGATTTCAACTCCACAACGAAGGATATTGTGCCCA
571622 TCTACACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACAACGAAGGATATTGTGCCCACAA
Found at i:571920 original size:240 final size:245
Alignment explanation
Indices: 571582--572112 Score: 736
Period size: 240 Copynumber: 2.2 Consensus size: 245
571572 GTGCCCACAA
** * *
571582 ATCCACGATTTCAACTTCACGGTGAAGGATATTGTGCCCATCTACACAATATTAGATTTCAACTT
1 ATCCACGATTTCAACTTCACGACGAAAGATATTGTGCCCA--TACACAAGATTAGATTTCAACTT
* *
571647 CACGATGAATGATATCAAATTCAAAGCTCAACTTCAC-GACGAAGGGGCTTCCCAGTTTCATTCA
64 CACGACGAAGGATATCAAATTCAAAGCTCAACTTCACAG-CGAAGGGGCTTCCCAGTTTCATTCA
* *
571711 GAGCCAATTTCAACTTCACGGCGAAGGATATTGGAATCGAAAC-A-ATACA-AGCTTGGATTTCA
128 GAGCCAATTTCAACTTCACGACGAAGGATATTGGAATCGAAACAACATACATAGATTGGATTTCA
* * * *
571773 ACTTCACGACGAAGGATATTCAAGTCAAGGCTGAACTTCACGACGAAGGGGCC
193 ACTTCACGACGAAGGATATCCAAGTCAAGGATCAACTTCACAACGAAGGGGCC
* *
571826 ATCCACGATTTCAACTTCACGACGAAAGATATTGTG-CCA-ACTCTAGATT-GTATTTCAACTTC
1 ATCCACGATTTCAACTTCACGACGAAAGATATTGTGCCCATACACAAGATTAG-ATTTCAACTTC
*
571888 ACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGA
65 ACGACGAAGGATATCAAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGA
* * * *
571953 GCCAATTTCAACTTCACGACGAATGATATTGGACTCGAAGCAACATTCATTTTCAGATTGGATTT
130 GCCAATTTCAACTTCACGACGAAGGATATTGGAATCGAAACAACATACA---T-AGATTGGATTT
*
572018 CAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTTCACAACGAAGGGGCC
191 CAACTTCACGACGAAGGATATCCAAGTCAAGGATCAACTTCACAACGAAGGGGCC
*
572073 ATCCACGATTTCAACTTCACGACG-AAGAATATCGTGCCCA
1 ATCCACGATTTCAACTTCACGACGAAAG-ATATTGTGCCCA
572113 CTAACAACAT
Statistics
Matches: 255, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
239 1 0.00
240 115 0.45
241 2 0.01
242 4 0.02
243 3 0.01
244 33 0.13
246 3 0.01
247 91 0.36
248 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (245 bp):
ATCCACGATTTCAACTTCACGACGAAAGATATTGTGCCCATACACAAGATTAGATTTCAACTTCA
CGACGAAGGATATCAAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGAG
CCAATTTCAACTTCACGACGAAGGATATTGGAATCGAAACAACATACATAGATTGGATTTCAACT
TCACGACGAAGGATATCCAAGTCAAGGATCAACTTCACAACGAAGGGGCC
Found at i:572179 original size:124 final size:124
Alignment explanation
Indices: 571993--572229 Score: 386
Period size: 124 Copynumber: 1.9 Consensus size: 124
571983 GGACTCGAAG
*
571993 CAACATTCATTTTCAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGATCAACTT
1 CAACATTCATTTTCAGATTGGATTTCAACTTCACGACGAAGGAAATCCAATTCAAGGATCAACTT
572058 CACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACTAA
66 CACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACTAA
* * * *
572117 CAACATTCATCTTT-AGATTGGATTTTAACTTCACGATGAATGAAATCCAATTCAAGGCTCAACT
1 CAACATTCAT-TTTCAGATTGGATTTCAACTTCACGACGAAGGAAATCCAATTCAAGGATCAACT
* * *
572181 TCACAACGAATGGGCCATCCACGATTTCAACTTCACGATGAAGGATATC
65 TCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGAATATC
572230 ATGTTCATTT
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 101 0.97
125 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (124 bp):
CAACATTCATTTTCAGATTGGATTTCAACTTCACGACGAAGGAAATCCAATTCAAGGATCAACTT
CACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGAATATCGTGCCCACTAA
Found at i:572375 original size:84 final size:83
Alignment explanation
Indices: 572234--572967 Score: 901
Period size: 84 Copynumber: 8.7 Consensus size: 83
572224 GATATCATGT
** * * * *
572234 TCATTTGCAGCATAGTTCAAGGCAAGAAAGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTA
* *
572299 TGCTCAGCTCCAAGGTACA
65 CGCTCAGCTCCAAGGCACA
*
572318 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAGAGTCCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAA-AGACCTTCGAGTTCGACTA
*
572383 CGCTCAGCTCCAAGGTACA
65 CGCTCAGCTCCAAGGCACA
* * * * * ** *
572402 TAATTTGCAACATAGCTCAAGGCAAGAATGACTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTA
*
572467 CGCTCAGCTCTAAGGCACA
65 CGCTCAGCTCCAAGGCACA
*
572486 TCATTTGCAGCATAACTCAAGGTTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTA
572551 CGCTCAGCTCCAAGGCACA
65 CGCTCAGCTCCAAGGCACA
*
572570 TCATTTGCAGCATAACTCAAGGCTAGAAGGTTTATCTGCCAACAAGAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAA-AGACCTTCGAGTTCGACTA
* *
572635 CGTTCAGCTCCAAGGCACT
65 CGCTCAGCTCCAAGGCACA
* * * * *
572654 TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTA
* *
572719 CGCTCAGCTCAAAGGCATA
65 CGCTCAGCTCCAAGGCACA
* * ** * *
572738 TAATTTGTAATATATCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGGCTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACTA
*
572803 CGCTCTGCTCCAAGGCACA
65 CGCTCAGCTCCAAGGCACA
* * * * *
572822 ACATTTGCAGCATAACTCAAGGTTAGAATGGTTATCTGCCAACAAAATACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAAC-AAAGACCTTCGAGTTCGACTA
* * *
572887 CACTTAGCTCAAAGGCACA
65 CGCTCAGCTCCAAGGCACA
* * * * * * * * *
572906 TCATTTACATCTTAGCTCAAGGCAAGAAAGGGTTATCTGTCAATAAAAACCGTCGAGTTCGA
1 TCATTTGCAGCATAACTCAAGGCTAG-AAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGA
572968 TTCCATTCTG
Statistics
Matches: 560, Mismatches: 82, Indels: 16
0.85 0.12 0.02
Matches are distributed among these distances:
83 6 0.01
84 534 0.95
85 20 0.04
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACA
Found at i:572679 original size:252 final size:251
Alignment explanation
Indices: 572234--572933 Score: 1015
Period size: 252 Copynumber: 2.8 Consensus size: 251
572224 GATATCATGT
** * * * * *
572234 TCATTTGCAGCATAGTTCAAGGCAAGAAAGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
572299 TGCTCAGCTCCAAGGTACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAG
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAA-GGTTATCTGCCAACAAG
* * * *
572364 AGTCCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATAATTTGCAACATAGCTCAAGGCAAGA
130 AGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGA
* *
572429 ATGACTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACA
195 AGGACTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACA
*
572486 TCATTTGCAGCATAACTCAAGGTTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
572551 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGTTTATCTGCCAACAAG
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGG-TTATCTGCCAACAAG
* *
572616 AGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACTTCATTTGCAACATAACTCAAGGCAAGA
130 AGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGA
* * *
572681 AGGGCTATTTGCCAACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCAAAGGCATA
195 AGGACTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACA
* * ** * *
572738 TAATTTGTAATATATCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGGCTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * * *
572803 CGCTCTGCTCCAAGGCACAACATTTGCAGCATAACTCAAGGTTAGAATGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAA-GGTTATCTGCCAACAAG
* * * * * * *
572868 ATACCTTCGAGTTCGATTACACTT-AGCTCAAAGGCACATCATTTACATCTTAGCTCAAGGCAAG
130 AGACCTTCGAGTTCGACTAC-GTTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAG
572932 AA
194 AA
572934 AGGGTTATCT
Statistics
Matches: 404, Mismatches: 41, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
251 2 0.00
252 398 0.99
253 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (251 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGTTATCTGCCAACAAGA
GACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAA
GGACTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACA
Found at i:575268 original size:28 final size:28
Alignment explanation
Indices: 575220--575273 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
575210 TCCCTTCAAA
* *
575220 TTTATTTAATATTTTTGTTATTTTTTAT
1 TTTATTTAATATTATTATTATTTTTTAT
575248 TTTATTTTAAT-TTATTATTATTTTTT
1 TTTA-TTTAATATTATTATTATTTTTT
575274 TCTTTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (28 bp):
TTTATTTAATATTATTATTATTTTTTAT
Found at i:575284 original size:28 final size:26
Alignment explanation
Indices: 575220--575304 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 26
575210 TCCCTTCAAA
* *
575220 TTTATTTAATATTTTTGTTATTTTTTAT
1 TTTATTTAAT-TTATTATTATTTTTT-T
575248 TTTATTTTAATTTATTATTATTTTTTT
1 TTTA-TTTAATTTATTATTATTTTTTT
** *
575275 CTTTCATTT-ATTTAACATTAATTTTTT
1 -TTT-ATTTAATTTATTATTATTTTTTT
575302 TTT
1 TTT
575305 CTTTTTCTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 3 0.06
27 16 0.33
28 23 0.47
29 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (26 bp):
TTTATTTAATTTATTATTATTTTTTT
Found at i:575315 original size:25 final size:27
Alignment explanation
Indices: 575264--575318 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
575254 TTAATTTATT
*
575264 ATTATTTTTTTCTTTCATTTATTTAAC
1 ATTAATTTTTTCTTTCATTTATTTAAC
575291 ATTAATTTTTT-TTTC-TTT-TTCTAAC
1 ATTAATTTTTTCTTTCATTTATT-TAAC
575316 ATT
1 ATT
575319 TTTTTGACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 10 0.38
26 4 0.15
27 10 0.38
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTAATTTTTTCTTTCATTTATTTAAC
Found at i:575386 original size:6 final size:6
Alignment explanation
Indices: 575377--575403 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
575367 GAATTGAATT
575377 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
575404 TCGCAATTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:581187 original size:3 final size:3
Alignment explanation
Indices: 581181--581224 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
581171 TATTAAGTAT
* *
581181 ATA ATA ATA ATA GTA ATA ATA ATA AT- ATA ATA ATA ATT ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
581225 TAAAACGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:581580 original size:53 final size:53
Alignment explanation
Indices: 581404--581605 Score: 264
Period size: 52 Copynumber: 3.8 Consensus size: 53
581394 GTATGACATT
* * * * * *
581404 GTTCCTTCATGATGAGGACGTCTGGTCATGTTTAAAGAT-AATTGAGATAACACG
1 GTTCCTTCGTGATGAGGACATCTGG-C-TATCTAAGGATGATTTGAGATAACACG
* * *
581458 GTTCCTTCGTGATGAGGACATCTGTCTATCTAAAGATGA-TTGAGATAATACG
1 GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACACG
*
581510 GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTTAGATAACACG
1 GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACACG
* *
581563 ATTCCTTCGTGATGAGGACATCTAGCTATCTAAGGATGATTTG
1 GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTG
581606 GCTCTTTCGT
Statistics
Matches: 133, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
52 58 0.44
53 53 0.40
54 22 0.17
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (53 bp):
GTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATTTGAGATAACACG
Found at i:581592 original size:105 final size:106
Alignment explanation
Indices: 581404--581603 Score: 280
Period size: 105 Copynumber: 1.9 Consensus size: 106
581394 GTATGACATT
* * * *
581404 GTTCCTTCATGATGAGGACGTCTGGTCATGTTTAAAGATAATTGAGATAACACGGTTCCTTCGTG
1 GTTCCTTCATGATGAGGACATCTGGTCATATCTAAAGATAATTGAGATAACACGATTCCTTCGTG
581469 ATGAGGACATCTGTCTATCTAAAGATGATTGAGATAATACG
66 ATGAGGACATCTGTCTATCTAAAGATGATTGAGATAATACG
* * * *
581510 GTTCCTTCGTGATGAGGACATCTGG-C-TATCTAAGGATGATTTTAGATAACACGATTCCTTCGT
1 GTTCCTTCATGATGAGGACATCTGGTCATATCTAAAGAT-AATTGAGATAACACGATTCCTTCGT
*
581573 GATGAGGACATCTAG-CTATCTAAGGATGATT
65 GATGAGGACATCT-GTCTATCTAAAGATGATT
581604 TGGCTCTTTC
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
104 8 0.10
105 51 0.61
106 24 0.29
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (106 bp):
GTTCCTTCATGATGAGGACATCTGGTCATATCTAAAGATAATTGAGATAACACGATTCCTTCGTG
ATGAGGACATCTGTCTATCTAAAGATGATTGAGATAATACG
Found at i:581799 original size:137 final size:136
Alignment explanation
Indices: 581510--581906 Score: 483
Period size: 137 Copynumber: 2.9 Consensus size: 136
581500 AGATAATACG
* * * *
581510 GTTCCTTCGTGATGAGGACATCTGGCTATC--TAAGGATGATTTTAGATAACACGATTCCTTCGT
1 GTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGAT-ATTTGAGATAACACG-TTCCTTCGT
* * ** * * *
581573 GATGAGGACATCTAGCTATCTAAGGATGATTTGGCTCTTTCGTGATGAGGAGTTCTGGTCGATGG
64 GATGAGGACGTCTGGCTATCTAAGGATGACATGGCTCATTCGTGATGAGGAGATCTGGTTGATGG
581638 ATGACATT
129 ATGACATT
* * * *
581646 ATTCCTTCATGATGAGGACGTCTGACCATCTTTAAAGATATTTGAGATAACACAGTTCCTTCATG
1 GTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACAC-GTTCCTTCGTG
* * * * * *
581711 ATGAGGACGTCTGGCTATCCAAGGATGGCGTGGCTCCTTCGTGCTGAGGAGATCTGGTTGGTGGA
65 ATGAGGACGTCTGGCTATCTAAGGATGACATGGCTCATTCGTGATGAGGAGATCTGGTTGATGGA
581776 TGACATT
130 TGACATT
* * * ** *
581783 GTTCCTTCGCGATGAGGACGTCTGGCCATTTTTAAAGATATTTGAGATAACATGGTTATTTTGTG
1 GTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACA-CGTTCCTTCGTG
* *
581848 ATGAGGACGTCTGGCTATCTAAGAATGACATGGCTCATTCGTGAAGAGGAGATCTGGTT
65 ATGAGGACGTCTGGCTATCTAAGGATGACATGGCTCATTCGTGATGAGGAGATCTGGTT
581907 ATCTAAGGAT
Statistics
Matches: 221, Mismatches: 36, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
136 25 0.11
137 189 0.86
138 7 0.03
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (136 bp):
GTTCCTTCGTGATGAGGACGTCTGGCCATCTTTAAAGATATTTGAGATAACACGTTCCTTCGTGA
TGAGGACGTCTGGCTATCTAAGGATGACATGGCTCATTCGTGATGAGGAGATCTGGTTGATGGAT
GACATT
Found at i:582730 original size:292 final size:292
Alignment explanation
Indices: 582206--582766 Score: 849
Period size: 292 Copynumber: 1.9 Consensus size: 292
582196 GTCTCAGAAT
* * *
582206 AAATGTTTCATTTATAGAACTCTTGCCACACTCAGAATTATGACCTTGTTGTACCCTTTTGTTCT
1 AAATGTTTCATTTATAGAACTCATGCCACACTCAAAATTATGACCTTGTTGTACCCTTTTGTTCA
*
582271 TGATAAAATCGACTTTCTTTGTCTGAACTTGTGTAGAAATCCAATAAAACTTTTTATCTTTGAAA
66 TGATAAAACCGACTTTCTTTGTCTGAACTTGTGTAGAAATCCAATAAAACTTTTTATCTTTGAAA
* * * * *
582336 GGAGAATCTACTATCTTTGTAAAATATAGATGTAAATATGCCAGACTCAGCAGAGATTAATTAGG
131 GGAGAATCTACTATCTTTGCAAAATATAGATGTAAATATGACAAACTCAACAAAGATTAATTAGG
* * * *
582401 AGAGTAGCGTCTATTTTAATTTGACTCTTGAAACACATCACAAGGAGGATTTATCCTAATTCCTT
196 AGAGTAGCGTATATTCTAATGTGACTCTTGAAACACATCACAAGGAGGATTTATCCTAATTCATT
582466 TCATGTCTCTACTTGTATTAAAGTCTTAAAAG
261 TCATGTCTCTACTTGTATTAAAGTCTTAAAAG
*
582498 AAATGTTTCATTTATATAACTCATGCCACACTCAAAATTATGACCTTGTTGTACCCATTTTGTTC
1 AAATGTTTCATTTATAGAACTCATGCCACACTCAAAATTATGACCTTGTTGTACCC-TTTTGTTC
** *
582563 ATGATAAAACCGGTTTTCTTT-TCATGAACTTGTGTAGAAATCCAATAAAGC-TTTTATCTTTGA
65 ATGATAAAACCGACTTTCTTTGTC-TGAACTTGTGTAGAAATCCAATAAAACTTTTTATCTTTGA
* *
582626 AAGGAGAATCTACTATCTTTGCAGAATGTAGATGTAAATATGACAAACTCAACAAAGATTAATTA
129 AAGGAGAATCTACTATCTTTGCAAAATATAGATGTAAATATGACAAACTCAACAAAGATTAATTA
* * * * * *
582691 GGATA-TCATCGTATGTTCTAATGTGACTTTTGAAACACATCACAAGGAGGATTTGTCTTAATTC
194 GGAGAGT-AGCGTATATTCTAATGTGACTCTTGAAACACATCACAAGGAGGATTTATCCTAATTC
582755 ATTTCATGTCTC
258 ATTTCATGTCTC
582767 CATATCTAAT
Statistics
Matches: 241, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
291 1 0.00
292 189 0.78
293 51 0.21
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (292 bp):
AAATGTTTCATTTATAGAACTCATGCCACACTCAAAATTATGACCTTGTTGTACCCTTTTGTTCA
TGATAAAACCGACTTTCTTTGTCTGAACTTGTGTAGAAATCCAATAAAACTTTTTATCTTTGAAA
GGAGAATCTACTATCTTTGCAAAATATAGATGTAAATATGACAAACTCAACAAAGATTAATTAGG
AGAGTAGCGTATATTCTAATGTGACTCTTGAAACACATCACAAGGAGGATTTATCCTAATTCATT
TCATGTCTCTACTTGTATTAAAGTCTTAAAAG
Found at i:586266 original size:19 final size:19
Alignment explanation
Indices: 586242--586280 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
586232 AATGTAGAGC
586242 AGCCTCTCGTGCTTCTAGT
1 AGCCTCTCGTGCTTCTAGT
586261 AGCCTCTCGTGCTTCTAGT
1 AGCCTCTCGTGCTTCTAGT
586280 A
1 A
586281 ACTTCTCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.13, C:0.31, G:0.21, T:0.36
Consensus pattern (19 bp):
AGCCTCTCGTGCTTCTAGT
Found at i:586287 original size:19 final size:19
Alignment explanation
Indices: 586244--586289 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
586234 TGTAGAGCAG
*
586244 CCTCTCGTGCTTCTAGTAG
1 CCTCTCGTGCTTCTAGTAA
586263 CCTCTCGTGCTTCTAGTAA
1 CCTCTCGTGCTTCTAGTAA
*
586282 CTTCTCGT
1 CCTCTCGT
586290 ACAACTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.11, C:0.33, G:0.17, T:0.39
Consensus pattern (19 bp):
CCTCTCGTGCTTCTAGTAA
Found at i:588555 original size:3 final size:3
Alignment explanation
Indices: 588549--588589 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
588539 TATTAAGTAT
* *
588549 ATA ATA ATA ATA GTA ATA ATA ATA AT- ATA ATA ATT ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
588590 TAAAACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:590220 original size:44 final size:44
Alignment explanation
Indices: 590048--590267 Score: 145
Period size: 44 Copynumber: 5.1 Consensus size: 44
590038 TAAAAATATT
* *
590048 AAATTAGGGG-CTTAAACTATAAAAGTAAAAAA-T-ATGATTG-AAA
1 AAATTAGGGGAC-TAAATTATAAATG-AAAAAAGTGA-GATTGAAAA
** * * *
590091 AAATTA-GGGACCCAATTATAAAGGTAAAAAGTGATATT--AAA
1 AAATTAGGGGACTAAATTATAAATGAAAAAAGTGAGATTGAAAA
* * * ** *
590132 AAA-CAGGGG-CATCAATTTTAACGGTAAAAAGTGAGATTGAAAAA
1 AAATTAGGGGAC-TAAATTATAAATGAAAAAAGTGAGATTG-AAAA
* * *
590176 AAATTAGGGGCCTAAATTATATAA-GAAAAAAATGGGATTGAAAA
1 AAATTAGGGGACTAAATTATA-AATGAAAAAAGTGAGATTGAAAA
* * *
590220 AAATTAGGGGACTCAATTATAAATGTAAATAGTGAGATTGAAAA
1 AAATTAGGGGACTAAATTATAAATGAAAAAAGTGAGATTGAAAA
590264 AAAT
1 AAAT
590268 CAAGAGTTTG
Statistics
Matches: 141, Mismatches: 24, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
40 2 0.01
41 37 0.26
42 16 0.11
43 10 0.07
44 49 0.35
45 25 0.18
46 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (44 bp):
AAATTAGGGGACTAAATTATAAATGAAAAAAGTGAGATTGAAAA
Found at i:590307 original size:130 final size:127
Alignment explanation
Indices: 590048--590396 Score: 312
Period size: 130 Copynumber: 2.7 Consensus size: 127
590038 TAAAAATATT
* * ** *
590048 AAATTAGGGGCTTAAACTATAAAAGTAAAAAATATGATTG-AAAAAATTAGGGACCCAATTATAA
1 AAATTAGGGGCATAAATTAT-AAAGTAAAAAATGGGATTGAAAAAAATTAGGGACTCAATTATAA
* * * * * *
590112 AGGTAAAAAGTGATATTAAAAAACAGGGGCATCAATTTTAACGGTAAAAAGTGAGATTGAAAAA
65 ATGTAAAAAGTGAGATTAAAAAACAAGAGCATCAATTATAAAGGTAAAAAGTGAGATTG-AAAA
* *
590176 AAATTAGGGGCCTAAATTATATAAGAAAAAAATGGGATTGAAAAAAATTAGGGGACTCAATTATA
1 AAATTAGGGGCATAAATTATA-AAGTAAAAAATGGGATTGAAAAAAATTA-GGGACTCAATTATA
* * ** ** *
590241 AATGTAAATAGTGAGATTGAAAAAAATCAAGAG-TTTGATTATAAAGGTTCAAGGTGAGATTG-A
64 AATGTAAAAAGTGAGATT--AAAAAA-CAAGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAA
590304 AA
126 AA
* * ** *
590306 AACTTATGATCATCAATTATAAATGTAAAAAATGGGATTGAAAAAAAATTAAGGG-CTTCAATTA
1 AAATTAGGGGCATAAATTATAAA-GTAAAAAATGGGATTG-AAAAAAATT-AGGGAC-TCAATTA
*
590370 TAAATATAAAAAGT-AGGATTACAAAAA
62 TAAATGTAAAAAGTGA-GATTA-AAAAA
590397 TTAGGGACCT
Statistics
Matches: 181, Mismatches: 28, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
127 1 0.01
128 33 0.18
129 12 0.07
130 68 0.38
131 35 0.19
132 28 0.15
133 4 0.02
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (127 bp):
AAATTAGGGGCATAAATTATAAAGTAAAAAATGGGATTGAAAAAAATTAGGGACTCAATTATAAA
TGTAAAAAGTGAGATTAAAAAACAAGAGCATCAATTATAAAGGTAAAAAGTGAGATTGAAAA
Found at i:590369 original size:45 final size:44
Alignment explanation
Indices: 590048--590413 Score: 202
Period size: 43 Copynumber: 8.5 Consensus size: 44
590038 TAAAAATATT
* * * * *
590048 AAATTAGGGGCTTAAACTATAAAAGTAAAAAAT-ATGATTG-AAA
1 AAATTAAGGGCTTCAATTATAAATGTAAAAAGTGA-GATTGAAAA
* * *
590091 AAATT-AGGGAC-CCAATTATAAAGGTAAAAAGTGATATT--AAA
1 AAATTAAGGG-CTTCAATTATAAATGTAAAAAGTGAGATTGAAAA
* * * * **
590132 AAA-CAGGGGCATCAATTTTAACGGTAAAAAGTGAGATTGAAAAA
1 AAATTAAGGGCTTCAATTATAAATGTAAAAAGTGAGATTG-AAAA
* * * * * *
590176 AAATTAGGGGCCTAAATTATATAA-GAAAAAAATGGGATTGAAAA
1 AAATTAAGGGCTTCAATTATA-AATGTAAAAAGTGAGATTGAAAA
* *
590220 AAATTAGGGGAC-TCAATTATAAATGTAAATAGTGAGATTGAAAA
1 AAATTAAGGG-CTTCAATTATAAATGTAAAAAGTGAGATTGAAAA
* * ** * ** *
590264 AAATCAAGAG-TTTGATTATAAAGGTTCAAGGTGAGATTG-AAA
1 AAATTAAGGGCTTCAATTATAAATGTAAAAAGTGAGATTGAAAA
* * ** * * *
590306 AACTTATGATCATCAATTATAAATGTAAAAAATGGGATTGAAAAA
1 AAATTAAGGGCTTCAATTATAAATGTAAAAAGTGAGATTG-AAAA
* *
590351 AAATTAAGGGCTTCAATTATAAATATAAAAAGT-AGGATT-ACAA
1 AAATTAAGGGCTTCAATTATAAATGTAAAAAGTGA-GATTGAAAA
*
590394 AAATT-AGGGACCTCAATTAT
1 AAATTAAGGG-CTTCAATTAT
590414 CAGGATAAAA
Statistics
Matches: 247, Mismatches: 59, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
40 1 0.00
41 32 0.13
42 35 0.14
43 67 0.27
44 51 0.21
45 60 0.24
46 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (44 bp):
AAATTAAGGGCTTCAATTATAAATGTAAAAAGTGAGATTGAAAA
Found at i:590410 original size:43 final size:44
Alignment explanation
Indices: 590318--590413 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
590308 CTTATGATCA
* * *
590318 TCAATTATAAATGTAAAAAATGGGATTGAAAAAAAATTAAGGGCT
1 TCAATTATAAATATAAAAAATAGGATT-AAAAAAAATTAAGGGCC
* *
590363 TCAATTATAAATATAAAAAGTAGGATT-ACAAAAATT-AGGGACC
1 TCAATTATAAATATAAAAAATAGGATTAAAAAAAATTAAGGG-CC
590406 TCAATTAT
1 TCAATTAT
590414 CAGGATAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 4 0.09
43 17 0.38
45 24 0.53
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (44 bp):
TCAATTATAAATATAAAAAATAGGATTAAAAAAAATTAAGGGCC
Found at i:593369 original size:12 final size:12
Alignment explanation
Indices: 593352--593378 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
593342 CTCAAAGCCC
593352 TAATTCCCTTTG
1 TAATTCCCTTTG
593364 TAATTCCCTTTG
1 TAATTCCCTTTG
593376 TAA
1 TAA
593379 ATTCTCCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (12 bp):
TAATTCCCTTTG
Found at i:598377 original size:107 final size:105
Alignment explanation
Indices: 598205--598422 Score: 348
Period size: 107 Copynumber: 2.1 Consensus size: 105
598195 TGGTTTCAAA
* * *
598205 TAATGATATTGTTAATGATGAAAAAATAAAAATAAATCATTCAAATGAGGTTTTAAACCTGGATC
1 TAATAATATTGTTAATGATGAAAAAATAAAAATAAATCATTCAAATGAGGTTTCAAACCTAGATC
*
598270 AATGGTGACATGTGTCACGATTTTATTGGATTGAAAATAAATT
66 AATGGTGACATGTGTCACGATTTGA-T--ATTGAAAATAAATT
*
598313 TAATAATATTGTTAATGATGAAAAAATAAAAA-AAATCATTCAAATGAGGTTTCAACCCTAGATC
1 TAATAATATTGTTAATGATGAAAAAATAAAAATAAATCATTCAAATGAGGTTTCAAACCTAGATC
*
598377 AATGGTGACATTTGTCACGATTTGATATTGAAAATAAATT
66 AATGGTGACATGTGTCACGATTTGATATTGAAAATAAATT
598417 TAATAA
1 TAATAA
598423 ATTAAAATAA
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
104 20 0.19
106 1 0.01
107 52 0.50
108 31 0.30
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (105 bp):
TAATAATATTGTTAATGATGAAAAAATAAAAATAAATCATTCAAATGAGGTTTCAAACCTAGATC
AATGGTGACATGTGTCACGATTTGATATTGAAAATAAATT
Found at i:600873 original size:34 final size:35
Alignment explanation
Indices: 600835--600912 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
600825 TACGAACAAA
* *
600835 CTTGTTTATAGTTCAT-AACTAGCTCGTTTAAAAG
1 CTTGTTTATAGTTCATGAACAAGCTCGTTCAAAAG
*
600869 CTTGTTTA-AGTTCATGAACAAGCTCGTTCACAAG
1 CTTGTTTATAGTTCATGAACAAGCTCGTTCAAAAG
*
600903 CTCGTTTATA
1 CTTGTTTATA
600913 TGTTTTAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 7 0.18
34 30 0.79
35 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (35 bp):
CTTGTTTATAGTTCATGAACAAGCTCGTTCAAAAG
Found at i:601139 original size:21 final size:22
Alignment explanation
Indices: 601086--601141 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
601076 ACAAAAAATA
601086 TTACTAATTTATTATATTATTAT
1 TTACT-ATTTATTATATTATTAT
601109 TTACTA-TTATTATA-TATT-T
1 TTACTATTTATTATATTATTAT
*
601128 TTATTAGTTTATTA
1 TTACTA-TTTATTA
601142 ATAAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.20
20 4 0.13
21 14 0.47
22 1 0.03
23 5 0.17
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TTACTATTTATTATATTATTAT
Found at i:602783 original size:2 final size:2
Alignment explanation
Indices: 602776--602808 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
602766 TTATGGCAGT
602776 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
602809 TATTTAATAT
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:604802 original size:14 final size:14
Alignment explanation
Indices: 604783--604812 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
604773 GTTATATATG
604783 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
604797 TGTGTGTGTGTGTA
1 TGTGTGTGTGTGTA
604811 TG
1 TG
604813 AGTTGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.43, T:0.50
Consensus pattern (14 bp):
TGTGTGTGTGTGTA
Found at i:605077 original size:22 final size:22
Alignment explanation
Indices: 605052--605101 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
605042 GTCCTTTAGA
*
605052 ACATATACACAGGTCCTTCGGG
1 ACATATACACAGGTCATTCGGG
* *
605074 ACATATGCATAGGTCATTCGGG
1 ACATATACACAGGTCATTCGGG
605096 ACATAT
1 ACATAT
605102 TTCATATGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
ACATATACACAGGTCATTCGGG
Found at i:613987 original size:15 final size:15
Alignment explanation
Indices: 613967--614002 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
613957 TTTAGTTGAC
613967 TTTTTCTTTACATTA
1 TTTTTCTTTACATTA
*
613982 TTTTTCTTTACTTTA
1 TTTTTCTTTACATTA
613997 TATTTT
1 T-TTTT
614003 AAATATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTCTTTACATTA
Found at i:616591 original size:23 final size:21
Alignment explanation
Indices: 616541--616619 Score: 76
Period size: 21 Copynumber: 3.7 Consensus size: 21
616531 AGGGTGTCAA
616541 AGTGCATCCATGCACC--CCTGT
1 AGTGCATCCATGCACCTGCC--T
616562 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTG-C-CT
*
616585 AGTGCATCGATGCACCATG--T
1 AGTGCATCCATGCACC-TGCCT
616605 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
616620 TCCATTTCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
23 16 0.31
24 3 0.06
25 1 0.02
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCTGCCT
Found at i:619796 original size:21 final size:21
Alignment explanation
Indices: 619770--619809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
619760 AAACAATTGG
619770 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
619791 TAACAATTGTTATCTTTTT
1 TAACAATTGATATCATTTT
619810 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:620082 original size:21 final size:21
Alignment explanation
Indices: 620034--620111 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
620024 GGTGTCAAAG
* * *
620034 TGCATTCATGCACCCCTTACAG
1 TGCATCCATGCACCCC-TGCAA
*
620056 TGCATCCATTCACCCCTGCAA
1 TGCATCCATGCACCCCTGCAA
*
620077 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCACCCCTGCAA
620098 TGCATCCATGCACC
1 TGCATCCATGCACC
620112 TGCCACTAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
21 36 0.72
22 14 0.28
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.23
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAA
Found at i:620126 original size:23 final size:20
Alignment explanation
Indices: 620054--620153 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 20
620044 CACCCCTTAC
* * *
620054 AGTGCATCCATTCACCCCTGC
1 AGTGCATCCATGCA-CCATGT
* * *
620075 AATGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCATGT
620096 AGTGCATCCATGCACC-TGCCACT
1 AGTGCATCCATGCACCATG----T
*
620119 AGTGCATCGATGCACCATGT
1 AGTGCATCCATGCACCATGT
620139 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
620154 TCCATTTCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.03
20 17 0.25
21 32 0.47
23 15 0.22
24 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCATGT
Found at i:626485 original size:2 final size:2
Alignment explanation
Indices: 626478--626519 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
626468 TTTTGAAAAC
626478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
626519 A
1 A
626520 GTTTTTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:626504 original size:107 final size:102
Alignment explanation
Indices: 626386--626596 Score: 243
Period size: 107 Copynumber: 2.0 Consensus size: 102
626376 TTTTATTTAG
* * *
626386 TATATGTATATAGTATATA-AT-ATATAGTTTTTTATAAA-A-TTTTGAAAACATATATGTAATA
1 TATATATATATA-TATATATATAATATAG-TTTTTAAAAATATTTTTG-AAA-ATATATATAATA
*
626447 TATAGT-TTTCTAAAAAAGACGTTTTGAAAACATATATATATATATA
62 TATA-TATTT-T-AAAAA-ACATTTT-AAAACATATATATA-ATATA
626493 TATATATATATATATATATATAATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATA
1 TATATATATATATATATATATAATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATA
**
626558 TATTTTTGAAAACATTTTAAAACATATATATAATATA
66 TATTTTAAAAAACATTTTAAAACATATATATAATATA
626595 TA
1 TA
626597 GGTTTTGAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
102 7 0.08
103 14 0.15
104 6 0.06
105 3 0.03
106 8 0.09
107 40 0.43
108 10 0.11
109 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (102 bp):
TATATATATATATATATATATAATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATA
TATTTTAAAAAACATTTTAAAACATATATATAATATA
Found at i:626585 original size:28 final size:27
Alignment explanation
Indices: 626530--626588 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
626520 GTTTTTAAAA
* * *
626530 ATATTTTTGAAAATATATATAATATAT
1 ATATTTTTGAAAACATATAAAACATAT
*
626557 ATATTTTTGAAAACATTTTAAAACATAT
1 ATATTTTTGAAAACA-TATAAAACATAT
626585 ATAT
1 ATAT
626589 AATATATAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (27 bp):
ATATTTTTGAAAACATATAAAACATAT
Found at i:626608 original size:77 final size:75
Alignment explanation
Indices: 626502--626685 Score: 296
Period size: 77 Copynumber: 2.4 Consensus size: 75
626492 ATATATATAT
*
626502 ATATATATATATAATATAGTTTTTAAAAATATTTTTGAAAATATATATAATATATATATTTTTGA
1 ATATATATA-AT-ATATAGTTTTTGAAAATATTTTTGAAAATATATATAATATATA-ATTTTTGA
626567 AAACATTTTAAAA
63 AAACATTTTAAAA
* *
626580 CATATATATAATATATAGGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTTGAAA
1 -ATATATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATATAATATATAATTTTTGAAA
*
626645 ACATTTTGAAA
65 ACATTTTAAAA
626656 ATATATATAATATATAGTTTTTGAAAATAT
1 ATATATATAATATATAGTTTTTGAAAATAT
626686 ATATGATATA
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
75 29 0.29
76 19 0.19
77 41 0.41
78 2 0.02
79 9 0.09
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (75 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTTGAAAATATATATAATATATAATTTTTGAAAA
CATTTTAAAA
Found at i:626677 original size:26 final size:26
Alignment explanation
Indices: 626648--626713 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
626638 TTTGAAAACA
626648 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
*
626674 TTTTGAAAATATATATGATATATAGT
1 TTTTGAAAATATATATAATATATAGT
626700 TTTTGAAAATATAT
1 TTTTGAAAATATAT
626714 TTATTTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:629522 original size:17 final size:19
Alignment explanation
Indices: 629493--629528 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
629483 AACAATTTTT
629493 TATTTTCA-TTTTTAAAAA
1 TATTTTCATTTTTTAAAAA
629511 TATTTT-ATTTTTTAAAAA
1 TATTTTCATTTTTTAAAAA
629529 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTCATTTTTTAAAAA
Found at i:635074 original size:20 final size:20
Alignment explanation
Indices: 635051--635092 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
635041 AAACAATGCT
635051 AATA-ATAAAAAATAAATAAA
1 AATAGATAAAAAA-AAATAAA
* *
635071 AATAGGTAAAAAAATATAAA
1 AATAGATAAAAAAAAATAAA
635091 AA
1 AA
635093 CTTAGGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAGATAAAAAAAAATAAA
Found at i:636491 original size:43 final size:42
Alignment explanation
Indices: 636396--636479 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 42
636386 TAAACGTTTC
* *
636396 AAAAC-ATATAATATATAAATTTTTAAAATGTTTTTTTTAAAA
1 AAAACTATATAATATATAAATTTTCAAAATG-TGTTTTTAAAA
*
636438 AAAACTATATATTATATAAATTTTCAAAATG-GTTTTTAAAA
1 AAAACTATATAATATATAAATTTTCAAAATGTGTTTTTAAAA
636479 A
1 A
636480 TTATATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.26
42 5 0.13
43 23 0.61
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (42 bp):
AAAACTATATAATATATAAATTTTCAAAATGTGTTTTTAAAA
Found at i:636553 original size:31 final size:34
Alignment explanation
Indices: 636496--636569 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 34
636486 TATATAAATG
* *
636496 TTTTCATAACGTTTTCAAAGTATATATA-TAT-A
1 TTTTCAAAACGTTTTCAAAGAATATATATTATAA
636528 TTTT-AAAACGTTTTCAAA-AACTATATATTATAA
1 TTTTCAAAACGTTTTCAAAGAA-TATATATTATAA
636561 TTTTCAAAA
1 TTTTCAAAA
636570 AATATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 1 0.03
31 19 0.53
32 7 0.19
33 5 0.14
34 4 0.11
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (34 bp):
TTTTCAAAACGTTTTCAAAGAATATATATTATAA
Found at i:636564 original size:33 final size:32
Alignment explanation
Indices: 636486--636569 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
636476 AAAATTATAT
* * * *
636486 TATATAAATGTTTTCATAACGTTTTCAAAGTA
1 TATATATATATTTTCAAAACGTTTTCAAACTA
636518 TATATATATATTTT-AAAACGTTTTCAAAAACTA
1 TATATATATATTTTCAAAACGTTTTC--AAACTA
636551 TATAT-TATAATTTTCAAAA
1 TATATATAT-ATTTTCAAAA
636570 AATATATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 10 0.23
32 15 0.34
33 15 0.34
34 4 0.09
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (32 bp):
TATATATATATTTTCAAAACGTTTTCAAACTA
Found at i:636611 original size:26 final size:25
Alignment explanation
Indices: 636567--636616 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
636557 ATAATTTTCA
*
636567 AAAAATATATTTTCAAAATGGTTTTT
1 AAAAATATATTATCAAAAT-GTTTTT
636593 AAAAATATATTAT-ATAAATGTTTT
1 AAAAATATATTATCA-AAATGTTTT
636617 CATAACGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (25 bp):
AAAAATATATTATCAAAATGTTTTT
Found at i:636620 original size:117 final size:119
Alignment explanation
Indices: 636457--636689 Score: 427
Period size: 117 Copynumber: 2.0 Consensus size: 119
636447 TATTATATAA
636457 ATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAG-TATA-
1 ATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAGATATAT
636520 TATATATATTTTAAAACGTTTTCAAAAACTATATATTATAATTTTCAAAAAATAT
66 TATATATATTTTAAAACGTTTTCAAAAACTATATA-TATAATTTTCAAAAAATAT
636575 ATTTTCAAAATGGTTTTTAAAAA-TATATTATATAAATGTTTTCATAACGTTTTCAAAGTATATA
1 ATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAG-ATATA
636639 TTATATATATTTTAAAACGTTTTCAAAAACTATATATATAATTTTCAAAAA
65 TTATATATATTTTAAAACGTTTTCAAAAACTATATATATAATTTTCAAAAA
636690 TATTTTAAAA
Statistics
Matches: 112, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
117 35 0.31
118 23 0.21
119 19 0.17
120 35 0.31
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (119 bp):
ATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAGATATAT
TATATATATTTTAAAACGTTTTCAAAAACTATATATATAATTTTCAAAAAATAT
Found at i:636637 original size:35 final size:34
Alignment explanation
Indices: 636589--636679 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 34
636579 TCAAAATGGT
* * *
636589 TTTTAAAAATATAT-TATATAAATGTTTTCATAACG
1 TTTTCAAAATATATAT-TATAAATATTTT-AAAACG
* *
636624 TTTTCAAAGTATATATTATATATATTTTAAAACG
1 TTTTCAAAATATATATTATAAATATTTTAAAACG
636658 TTTTCAAAA-ACTATATATATAA
1 TTTTCAAAATA-TATAT-TATAA
636680 TTTTCAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
33 1 0.02
34 18 0.39
35 26 0.57
36 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (34 bp):
TTTTCAAAATATATATTATAAATATTTTAAAACG
Found at i:636725 original size:35 final size:34
Alignment explanation
Indices: 636571--636757 Score: 145
Period size: 33 Copynumber: 5.4 Consensus size: 34
636561 TTTTCAAAAA
636571 ATATATTTTCAAAATGGTTTTTAAAAA-TATATTATAT
1 ATATATTTTCAAAAT-G-TTTTAAAAACTATA--ATAT
* * * * * *
636608 AAATGTTTTCATAACGTTTTCAAAGTA-TATATTAT
1 ATATATTTTCAAAATGTTTT-AAA-AACTATAATAT
*
636643 ATATATTTT-AAAACGTTTTCAAAAACTAT-ATAT
1 ATATATTTTCAAAATGTTTT-AAAAACTATAATAT
*
636676 ATA-ATTTTCAAAAATATTTTAAAAACTATAAATAT
1 ATATATTTTC-AAAATGTTTTAAAAACTAT-AATAT
*
636711 ACATATTTTCAAAATGTTTT--AAACTATATATAT
1 ATATATTTTCAAAATGTTTTAAAAACTATA-ATAT
*
636744 ATGTATTTTCAAAA
1 ATATATTTTCAAAA
636758 ACAATTTGCA
Statistics
Matches: 124, Mismatches: 17, Indels: 22
0.76 0.10 0.13
Matches are distributed among these distances:
32 6 0.05
33 39 0.31
34 24 0.19
35 29 0.23
36 10 0.08
37 16 0.13
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (34 bp):
ATATATTTTCAAAATGTTTTAAAAACTATAATAT
Found at i:637567 original size:165 final size:165
Alignment explanation
Indices: 637372--638179 Score: 783
Period size: 165 Copynumber: 4.9 Consensus size: 165
637362 AAGTTGAATA
** * * * * * *
637372 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTGTTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
* ** * * *
637437 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGA
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAA
*
637501 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
130 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* * * * **
637537 TAATCGAACTCGGGGGTGTTTGGAAGATAGCCCTTCTCGACTTAAGTTGTGCTATAAATGATATG
1 TAATCGAACTCGGGGGTGTTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
* *
637602 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
* *
637667 GTATGTTGCAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* * *
637702 TAATCGAACTCGGGGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGCTGCAAATGA
1 TAATCGAACTCGGGGG----TGTTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * * * ** *
637767 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGAC
62 TATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
* * * *
637828 TTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCG
126 TTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
* ** * * *
637867 TAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGA
1 TAATCGAACTCG--GG-GGTGT-TTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* *
637932 TATGCCTTGGAACTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
62 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
637997 TAAGTTATGCTGCAAATGATGTGCCCTC-AGAGCTGAGTG
127 TAAGTTATGCTGCAAATGATGTGCCCTCGA-AGCTGAGTG
** * * * * * * *
638036 TAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGA
1 TAATCGAACTCGGGGGT-GTTTGG---CAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * * * * ** *
638101 TGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGAC
62 TATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC
* *
638162 TTAAGCTATGCTGTAAAT
126 TTAAGTTATGCTGCAAAT
638180 AGTTTGTTTA
Statistics
Matches: 535, Mismatches: 87, Indels: 41
0.81 0.13 0.06
Matches are distributed among these distances:
164 33 0.06
165 219 0.41
166 84 0.16
167 4 0.01
168 46 0.09
169 96 0.18
170 53 0.10
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGGGGGTGTTTGGCAGACAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
TTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:637720 original size:85 final size:85
Alignment explanation
Indices: 637372--638179 Score: 843
Period size: 85 Copynumber: 9.7 Consensus size: 85
637362 AAGTTGAATA
* * *
637372 TAATCGAACTCGAAGGTC--T--TTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * *
637433 TGTG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGTG
* * ** * * * *
637452 GAGTCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
1 TAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
637516 ATGTGCCCTCGAAGCTGAGTG
65 ATGTGCCCTCGAAGCTGAGTG
** * * * * **
637537 TAATCGAACTCG--GG--GGTGTTTGGAAGATAGCCCTTCTCGACTTAAGTTGTGCTATAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * *
637598 TATG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGTG
* * * * *
637617 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGTTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
637682 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGTG
** * * *
637702 TAATCGAACTCGGGGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
637767 TGTGCCCTCGAAGCTGAGTG
66 TGTGCCCTCGAAGCTGAGTG
** * *
637787 TAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * *
637848 TGTG-CCTTGGAGCTGAGCG
66 TGTGCCCTCGAAGCTGAGTG
* * * * *
637867 TAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * *
637932 TATGCCTTGGAA-CTGAGTG
66 TGTGCCCTCGAAGCTGAGTG
*
637951 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
638016 TGTGCCCTC-AGAGCTGAGTG
66 TGTGCCCTCGA-AGCTGAGTG
** * * * * *
638036 TAATCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATG
1 TAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
638100 ATGTGCCCTCGAAGCTGAGTG
65 ATGTGCCCTCGAAGCTGAGTG
* ** * * *
638121 TAATCAAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAAT
1 TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
638180 AGTTTGTTTA
Statistics
Matches: 608, Mismatches: 98, Indels: 43
0.81 0.13 0.06
Matches are distributed among these distances:
80 68 0.11
81 108 0.18
82 4 0.01
83 5 0.01
84 189 0.31
85 228 0.38
86 6 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (85 bp):
TAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
TGTGCCCTCGAAGCTGAGTG
Found at i:637759 original size:250 final size:250
Alignment explanation
Indices: 637402--638179 Score: 951
Period size: 250 Copynumber: 3.1 Consensus size: 250
637392 TAGCAGATAG
* * * *
637402 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGGAGTCGAACTCGAA
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAA
** * * * *
637466 GGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAG
66 GGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAG
* * * *
637530 CTGAGTGTAATCGAACTCGGGGGTGTTTGGAAGATAGCCCTTCTCGACTTAAGTTGTGCTATAAA
130 CTGAGTGTAATCGAACTCGGGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTACAAA
637595 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAA
195 TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAA
* * * * **
637651 CCCTTCTCGACTTCAGGTATGTTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAA
* * *
637716 GGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGCTGCAAATGATGTGCCCTCGAAGC
66 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGC
* *
637781 TGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
131 TGAGTGTAATCGAACTCGGGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTACAAAT
* *
637846 GATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAA
196 GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAA
* * * * * *
637901 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAA-CTGAGTGTAGTCGAACTCGAA
1 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAA
637965 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTC-AGAG
66 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA-AG
** * * * * * * *
638029 CTGAGTGTAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTG
130 CTGAGTGTAATCGAACTCGGGGGTC-TTTGG--A-AGATAGCCCTTCTCGACTTAAGCTATGCTA
* * * * * * * ** * *
638094 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTC--T--TTGGCAGATAG
191 CAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAA
*
638151 CCCTTCTCGACTTAAGCTATGCTGTAAAT
1 CCCTTCTCGACTTAAGCTATGCTGCAAAT
638180 AGTTTGTTTA
Statistics
Matches: 458, Mismatches: 63, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
248 1 0.00
249 137 0.30
250 259 0.57
252 1 0.00
253 34 0.07
254 26 0.06
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (250 bp):
CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCGAACTCGAA
GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGC
TGAGTGTAATCGAACTCGGGGGTCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTACAAAT
GATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGACAA
Found at i:637932 original size:334 final size:331
Alignment explanation
Indices: 637372--638179 Score: 1029
Period size: 334 Copynumber: 2.4 Consensus size: 331
637362 AAGTTGAATA
* * *
637372 TAATCGAACTCGAAGGTC-TTTAG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTTGGTCACAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * * ** * * *
637433 TGTG-CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCC
66 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGG---CAGATAGCCCTTCTCGAC
* * * *
637497 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTGTTTGGAA
127 TTAAGCTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGGGCGTGTTTGGAA
* * * * *
637562 GATAGCCCTTCTCGACTTAAGTTGTGCTATAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACT
192 GACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTTGGAACTGAGCGTAGTCGAACT
* *
637627 CGAAGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGTTGCAAATGATGTGCCCTC-
257 CGAAGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTAAGGTATGCTGCAAATGATGTGCCCTCA
637691 GAAGCTGAGTG
322 G-AGCTGAGTG
** ** * *
637702 TAATCGAACTCGGGGGTC-TTTGGTTGGCAGACAACCCTTCTCGACTTCAGGTATGCTGCAAATG
1 TAATCGAACTCGAAGGTCTTTTGG-TCACAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATG
637766 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTA
65 ATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTA
* * * * * * *
637831 AGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGC
130 AGCTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCG--GG-CGTGT-TTGGA
* *
637895 AGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAACTGAGTGTAGTCGAAC
191 AGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTTGGAACTGAGCGTAGTCGAAC
* *
637960 TCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTC
256 TCGAAGGTCTTTGGTTGGCAGACAACCCTTCTCGACTTAAGGTATGCTGCAAATGATGTGCCCTC
638025 AGAGCTGAGTG
321 AGAGCTGAGTG
* * * * * * *
638036 TAATCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGA
1 TAATCGAACTCGAAGGTCTTTTGGTCACAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
*
638101 TGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
66 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
638166 GCTATGCTGTAAAT
131 GCTATGCTGTAAAT
638180 AGTTTGTTTA
Statistics
Matches: 415, Mismatches: 52, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
330 43 0.10
331 36 0.09
332 2 0.00
333 2 0.00
334 300 0.72
335 32 0.08
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (331 bp):
TAATCGAACTCGAAGGTCTTTTGGTCACAGACAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
GCTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCGGGCGTGTTTGGAAGACA
ACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAA
GGTCTTTGGTTGGCAGACAACCCTTCTCGACTTAAGGTATGCTGCAAATGATGTGCCCTCAGAGC
TGAGTG
Found at i:641595 original size:18 final size:19
Alignment explanation
Indices: 641554--641598 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
641544 AGTTAATGTG
641554 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
* *
641573 AATGCACAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
641591 AATGCAAA
1 AATGCAAA
641599 ATGTCTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.64, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:644658 original size:26 final size:27
Alignment explanation
Indices: 644612--644662 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
644602 ATAAATAATA
644612 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
644640 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
644663 TGTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:644668 original size:36 final size:36
Alignment explanation
Indices: 644624--644812 Score: 141
Period size: 36 Copynumber: 5.1 Consensus size: 36
644614 ATATATATAT
*
644624 AAACGTTTTCAAAAACATATAATATATAAATTTTTA
1 AAACGTTTTCAAAAACATATATTATATAAATTTTTA
* * * * * *
644660 AAATGTTTTTTAAAAAAAAAACTATATATTATATATTTTCA
1 AAACG--TTTTCAAAAACATA-TAT-TA-TATAAATTTTTA
* * *
644701 AAATGGTTTTTAAAAA-TTATATTATATAAATGTTTTCA
1 AAA-CGTTTTCAAAAACATATATTATATAAAT-TTTT-A
* ** *
644739 TAACGTTTTCAAAAGTATATATTATATATA-TTTTA
1 AAACGTTTTCAAAAACATATATTATATAAATTTTTA
*
644774 AAACGTTTTCAAAAACTATATATTATAT-AATTTTCA
1 AAACGTTTTCAAAAAC-ATATATTATATAAATTTTTA
644810 AAA
1 AAA
644813 AATATATTTT
Statistics
Matches: 118, Mismatches: 24, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
35 15 0.13
36 32 0.27
37 14 0.12
38 29 0.25
39 3 0.03
40 11 0.09
41 13 0.11
42 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (36 bp):
AAACGTTTTCAAAAACATATATTATATAAATTTTTA
Found at i:644728 original size:41 final size:41
Alignment explanation
Indices: 644634--644716 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
644624 AAACGTTTTC
* *
644634 AAAAAC-ATATAATATATAAATTTTTAAAATGTTTTTTAAAAA
1 AAAAACTATAT-AT-TATAAATTTTCAAAATGGTTTTTAAAAA
*
644676 AAAAACTATATATTATATATTTTCAAAATGGTTTTTAAAAA
1 AAAAACTATATATTATAAATTTTCAAAATGGTTTTTAAAAA
644717 TTATATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 25 0.68
42 8 0.22
43 4 0.11
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (41 bp):
AAAAACTATATATTATAAATTTTCAAAATGGTTTTTAAAAA
Found at i:644737 original size:38 final size:37
Alignment explanation
Indices: 644624--644803 Score: 145
Period size: 38 Copynumber: 4.8 Consensus size: 37
644614 ATATATATAT
* *
644624 AAACGTTTTCAAAAACATATAATATATAAAT-TTTTA
1 AAACGTTTTCAAAAATATATATTATATAAATATTTTA
* * * * *
644660 AAATGTTTTTTAAAAA-AAAAACTATATATTATATATTTTCA
1 AAACG-TTTTCAAAAATATATA-T-TATA-TAAATATTTT-A
* * *
644701 AAATGGTTTTTAAAAAT-TATATTATATAAATGTTTTCA
1 AAA-CGTTTTCAAAAATATATATTATATAAATATTTT-A
* *
644739 TAACGTTTTCAAAAGTATATATTATAT--ATATTTTA
1 AAACGTTTTCAAAAATATATATTATATAAATATTTTA
644774 AAACGTTTTCAAAAACTATATATTATATAA
1 AAACGTTTTCAAAAA-TATATATTATATAA
644804 TTTTCAAAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
35 14 0.12
36 25 0.22
37 19 0.17
38 26 0.23
39 8 0.07
40 5 0.04
41 16 0.14
42 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (37 bp):
AAACGTTTTCAAAAATATATATTATATAAATATTTTA
Found at i:644797 original size:27 final size:25
Alignment explanation
Indices: 644762--644864 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 25
644752 AGTATATATT
*
644762 ATATATATTTTAAAACGTTTTCAAAA
1 ATATATATTATAAAA-GTTTTCAAAA
*
644788 ACTATATATTATATAA-TTTTCAAAA
1 A-TATATATTATAAAAGTTTTCAAAA
* *
644813 A-ATATATTTTCAAAATGGTTTTTAAAA
1 ATATATATTAT-AAAA--GTTTTCAAAA
644840 ATTATATATTATATAAATGTTTTCA
1 A-TATATATTATA-AAA-GTTTTCA
644865 TAACGTTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
23 8 0.13
24 3 0.05
25 10 0.16
26 1 0.02
27 21 0.34
28 7 0.11
29 11 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATATATTATAAAAGTTTTCAAAA
Found at i:644823 original size:15 final size:16
Alignment explanation
Indices: 644798--644827 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
644788 ACTATATATT
644798 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
644814 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
644828 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:644876 original size:126 final size:125
Alignment explanation
Indices: 644690--644940 Score: 477
Period size: 126 Copynumber: 2.0 Consensus size: 125
644680 ACTATATATT
644690 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
644755 ATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
644814 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAA-T-TATATTATATAAATGTTTTCATAACGTTTTCAAAA
644879 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
64 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
644941 TATTTTAAAA
Statistics
Matches: 124, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
124 27 0.22
125 1 0.01
126 55 0.44
127 41 0.33
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (125 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Done.