Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008098.1 Hibiscus syriacus cultivar Beakdansim tig00110622_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: 522112
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 3 of 3
Found at i:435529 original size:20 final size:20
Alignment explanation
Indices: 435484--435596 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
435474 GCGTTGCGAT
* *
435484 TTTCTCGTTGTGATAGTC-A
1 TTTCGCGTTGCGATAGTCAA
435503 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
*
435523 ATTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAA
* * *
435543 ATTCGCGTTGCGATAATCAT
1 TTTCGCGTTGCGATAGTCAA
* *
435563 TTTCGCGTTGCGATAATCAT
1 TTTCGCGTTGCGATAGTCAA
*
435583 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
435597 TTTAAGTTTC
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
19 16 0.19
20 70 0.81
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAA
Found at i:435606 original size:20 final size:20
Alignment explanation
Indices: 435583--435626 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
435573 CGATAATCAT
435583 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
435603 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
435623 TTTC
1 TTTC
435627 AGAAACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:435607 original size:40 final size:40
Alignment explanation
Indices: 435504--435616 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
435494 TGATAGTCAT
* * *
435504 TTCGCGTTGCGATAGTCAA-ATTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAAT-AAGTTTCGCGTTGCGATAATCAAA
* * **
435544 TTCGCGTTGCGATAATCATTTTCGCGTTGCGATAATCATT
1 TTCGCGTTGCGATAATAAGTTTCGCGTTGCGATAATCAAA
* ** *
435584 TTCGTGTTGCGATTTTAAGTTTCGTGTTGCGAT
1 TTCGCGTTGCGATAATAAGTTTCGCGTTGCGAT
435617 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.02
40 59 0.98
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
TTCGCGTTGCGATAATAAGTTTCGCGTTGCGATAATCAAA
Found at i:436199 original size:21 final size:21
Alignment explanation
Indices: 436104--436206 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
436094 GCCCAACTCA
436104 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
436125 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* * ** *
436146 TCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
** *
436167 CCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
*
436188 CCTGTCATCGTTGAAGAGG
1 CCTGTCATCGTTCAAGAGG
436207 TCTCTCCCAA
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:436205 original size:42 final size:42
Alignment explanation
Indices: 436104--436215 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
436094 GCCCAACTCA
* * *
436104 CCTGTCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * ** *
436146 TCTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
* * *
436188 CCTGTCATCGTTGAAGAGGTCTCTCCCA
1 CCTGTCATCGTTCAAGAGGCCCCTCCCA
436216 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCC
Found at i:437669 original size:36 final size:30
Alignment explanation
Indices: 437589--437654 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
437579 ATAAGAGTTG
*
437589 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
437619 ATTTGTTTAATTGATGTGTAAATAATTATT
1 ATTTGTTTAATTGATGTGTAAATAATTATT
437649 ATTTGT
1 ATTTGT
437655 GCTTATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTATT
Found at i:437741 original size:54 final size:54
Alignment explanation
Indices: 437627--437741 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
437617 TTATTTGTTT
* *
437627 AATTGATGTGTAAATAATTATTATTTGTGCTTATTTAATTGATTAAAAATTTAT
1 AATTGATGTGTAAATAATTATTATTTGTGCTTATTTAATTGATTAAAAATGTAA
* * * *
437681 TATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAATTGATT-GAAATGTAA
1 AATTGATGTGTAAATAATTATTATTTGTGCTTATTTAATTGATTAAAAATGTAA
437734 AAGTTGAT
1 AA-TTGAT
437742 TTGTTGATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
53 7 0.13
54 46 0.87
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.49
Consensus pattern (54 bp):
AATTGATGTGTAAATAATTATTATTTGTGCTTATTTAATTGATTAAAAATGTAA
Found at i:437832 original size:20 final size:20
Alignment explanation
Indices: 437804--438061 Score: 142
Period size: 20 Copynumber: 13.8 Consensus size: 20
437794 GCGATTTTCT
437804 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCC
* * *
437824 CGTTACGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCC
* *
437844 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCC
*
437863 TGTTGCGAT--T---A-TCTC
1 CGTTGCGATAGTCAAATTC-C
* * *
437878 AG-TGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCC
** *
437897 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCC
** *
437917 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCC
*
437937 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCC
*
437951 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCC
** *
437971 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCC
*
437991 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCC
* *
438005 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCC
* *
438025 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCC
438045 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
438062 GAATGTGTAA
Statistics
Matches: 186, Mismatches: 32, Indels: 40
0.72 0.12 0.16
Matches are distributed among these distances:
14 27 0.15
15 1 0.01
16 3 0.02
17 1 0.01
18 2 0.01
19 17 0.09
20 135 0.73
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCC
Found at i:437955 original size:54 final size:54
Alignment explanation
Indices: 437897--438053 Score: 260
Period size: 54 Copynumber: 2.9 Consensus size: 54
437887 GTCAAATTCG
**
437897 CGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
437951 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
* * * *
438005 CGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
438054 AGTCAAATGA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCC
Found at i:437968 original size:74 final size:74
Alignment explanation
Indices: 437761--437999 Score: 286
Period size: 74 Copynumber: 3.2 Consensus size: 74
437751 TCAATCTGCA
* * * * * * *
437761 TCATATTCGCGTTGCGATAGTC-TAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCC
1 TCATATTCGCGTTGCGATAGTCAT-TTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGC
* *
437825 GTTACGATAA
65 GTTGCGATAG
* ** * *
437835 TCAAATTCGCGTTGCGATAGTCA-TTTCGTGTTGCGATTATCTCAG-TGTGATAGTCAAATTCGC
1 TCATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATC-CCGTTGCGATAGTCAAATTCGC
437898 GTTGCGATAG
65 GTTGCGATAG
*
437908 TCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCG
1 TCATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCG
437973 TTGCGATAG
66 TTGCGATAG
* *
437982 TCATTTTCGCATTGCGAT
1 TCATATTCGCGTTGCGAT
438000 TATCCCGTTG
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
73 59 0.42
74 82 0.58
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (74 bp):
TCATATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCG
TTGCGATAG
Found at i:438029 original size:74 final size:74
Alignment explanation
Indices: 437804--438058 Score: 241
Period size: 74 Copynumber: 3.5 Consensus size: 74
437794 GCGATTTTCT
* * * ** * * **
437804 CGTTGCGATAGTCAAATTCCCGTTACGATAATCAAATTCGCGTTGCGATAGTCA-TTTCGTGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAGTTGCGCATTG
* * *
437868 CGATTATCT
66 CAAATATCA
* * * *
437877 CAG-TGTGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATT
1 C-GTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAGTTGCGCATT
* * *
437941 GCGATTATCC
65 GCAAATATCA
*
437951 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA-TCCCGTTGCG-AT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGA-TAGT-CAGTTGCGCAT
*
438014 ATTCAAAT-TCA
64 -TGCAAATATCA
*
438025 CGTTGCGATAGTCATATTCGCGTTGCGATAGTCA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCA
438059 AATGAATGTG
Statistics
Matches: 157, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
73 47 0.30
74 99 0.63
75 11 0.07
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATAGTCAGTTGCGCATTG
CAAATATCA
Found at i:438259 original size:18 final size:18
Alignment explanation
Indices: 438236--438270 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
438226 AAGCCGGTTG
438236 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
438254 TGATTGCGATTTTGATT
1 TGATTGAGATTTTGATT
438271 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:441432 original size:20 final size:20
Alignment explanation
Indices: 441360--441428 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
441350 ATCACGTATT
441360 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
441380 ATCTCGTTGCGATAGTCCGA
1 ATCGCGTTGCGATAGTCAGA
*
441400 ATCGCGTTGTGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
441420 ATCGCGTTG
1 ATCGCGTTG
441429 TGATCACGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:441521 original size:21 final size:19
Alignment explanation
Indices: 441462--441527 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
441452 ATTTACATAT
*
441462 TCGCATTGCGATTATCTAAAA
1 TCGCAATGCGA-TATC-AAAA
* * *
441483 TCACAACGCGGATTTCAAAAA
1 TCGCAATGC-GATATC-AAAA
441504 TCGCAATGCGATGATCAAAA
1 TCGCAATGCGAT-ATCAAAA
441524 TCGC
1 TCGC
441528 GTTGCGAATC
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
20 11 0.31
21 22 0.63
22 2 0.06
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATATCAAAA
Found at i:442323 original size:2 final size:2
Alignment explanation
Indices: 442316--442342 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
442306 TTAATTTCAA
442316 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
442343 ATTACATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:443939 original size:18 final size:18
Alignment explanation
Indices: 443916--443950 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
443906 ATATGAAATT
*
443916 TGTCCCGATGGACCACTA
1 TGTCCCGAAGGACCACTA
443934 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
443951 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:444227 original size:30 final size:30
Alignment explanation
Indices: 444193--444275 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
444183 AATTCACATA
444193 TCACATATCTCATGTCATATTCTCATATGG
1 TCACATATCTCATGTCATATTCTCATATGG
* * * * *
444223 TCACATAGCTCATATCACTTAATCTCTTATGT
1 TCACATATCTCATGTCA--TATTCTCATATGG
*
444255 TCACATATCACATGTTCATAT
1 TCACATATCTCATG-TCATAT
444276 CATTCCTTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
30 15 0.37
31 2 0.05
32 21 0.51
33 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
TCACATATCTCATGTCATATTCTCATATGG
Found at i:446592 original size:30 final size:29
Alignment explanation
Indices: 446520--446594 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
446510 TTTAAAATGT
446520 TTAAAATATTTTTTTTATCAAAATAAATA
1 TTAAAATATTTTTTTTATCAAAATAAATA
* ***
446549 TCTAAAGAT-TTTTTTTTATTAAAATGTGTA
1 T-TAAA-ATATTTTTTTTATCAAAATAAATA
446579 CTTAAAATATTTTTTT
1 -TTAAAATATTTTTTT
446595 AATCTTAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 3 0.08
30 32 0.84
31 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (29 bp):
TTAAAATATTTTTTTTATCAAAATAAATA
Found at i:452592 original size:32 final size:32
Alignment explanation
Indices: 452522--452584 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
452512 TTAATTAAAC
*
452522 AAACGAACATAAATGAGTGAATTACCGAACGA
1 AAACGAACATAAATGAATGAATTACCGAACGA
* *
452554 AAACGAACATAAATGAATGGATTATCGAACG
1 AAACGAACATAAATGAATGAATTACCGAACG
452585 TTCACGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.17
Consensus pattern (32 bp):
AAACGAACATAAATGAATGAATTACCGAACGA
Found at i:455813 original size:31 final size:31
Alignment explanation
Indices: 455778--455850 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
455768 AGGTTAATTT
455778 TTTAATTTAA-TCTCTAAAATTGAGATAAAAA
1 TTTAATTTAACTC-CTAAAATTGAGATAAAAA
* * *
455809 TTTAATGTAACTCCTAAACTTTAGATAAAAA
1 TTTAATTTAACTCCTAAAATTGAGATAAAAA
*
455840 TATCAATTTAA
1 T-TTAATTTAA
455851 ACTATAGATC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 26 0.74
32 9 0.26
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (31 bp):
TTTAATTTAACTCCTAAAATTGAGATAAAAA
Found at i:456744 original size:31 final size:31
Alignment explanation
Indices: 456702--456785 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
456692 AATTTAGGGA
* *
456702 TTAAATTGATATTTTATCTAAAGTTTA-AGAG
1 TTAAATAGATATTTTATCTAAAATTTATAG-G
*
456733 TTAAATAGATATTATATCTAAAATTTATAGG
1 TTAAATAGATATTTTATCTAAAATTTATAGG
* *
456764 TCAAATTAG-GATTTTATCTAAA
1 TTAAA-TAGATATTTTATCTAAA
456786 CTTCAATGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 40 0.89
32 5 0.11
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.43
Consensus pattern (31 bp):
TTAAATAGATATTTTATCTAAAATTTATAGG
Found at i:466639 original size:51 final size:48
Alignment explanation
Indices: 466563--466663 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 48
466553 TTTATTCATT
466563 CATATGCTCAACTGTGGATTAACACATGCTTGAAGTACTGAATGAGTAGCC
1 CATATGCTCAACTGTGGATTAACACATGCTTGAAG---TGAATGAGTAGCC
466614 CATATGCTCAACTGTGGATTAACACATGCTTGAAGTGAATGAGTAGCC
1 CATATGCTCAACTGTGGATTAACACATGCTTGAAGTGAATGAGTAGCC
466662 CA
1 CA
466664 AGCTAAAAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
48 15 0.30
51 35 0.70
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (48 bp):
CATATGCTCAACTGTGGATTAACACATGCTTGAAGTGAATGAGTAGCC
Found at i:474464 original size:81 final size:81
Alignment explanation
Indices: 474321--474485 Score: 260
Period size: 81 Copynumber: 2.0 Consensus size: 81
474311 AATTTATATG
* *
474321 TTTTGTGTTCGATTAAATTAGATAGAAGTATAAAGCTTGAAGGTTAAAGAAATCAGCTTGAGCAA
1 TTTTATGTTCGAGTAAATTAGATAGAAG--TAAAGCTTGAAGGTTAAAGAAATCAGCTTGAGCAA
474386 TACAGATTTGAATGTGGAA
64 TACAGA-TTGAATGTGGAA
*
474405 TTTTATGTTCGAGTAAATTAGGTAGAAG-AAAGCTTGAAGGTTAAAGAAATCAGCTTGAGCAATA
1 TTTTATGTTCGAGTAAATTAGATAGAAGTAAAGCTTGAAGGTTAAAGAAATCAGCTTGAGCAATA
*
474469 CAGATTGGATGTGGAA
66 CAGATTGAATGTGGAA
474485 T
1 T
474486 GAGTTTTTGG
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
80 12 0.16
81 40 0.52
84 25 0.32
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (81 bp):
TTTTATGTTCGAGTAAATTAGATAGAAGTAAAGCTTGAAGGTTAAAGAAATCAGCTTGAGCAATA
CAGATTGAATGTGGAA
Found at i:474734 original size:21 final size:22
Alignment explanation
Indices: 474703--474744 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
474693 ATATAATTAA
474703 ATTTTTTAAA-TATTA-ATAAG
1 ATTTTTTAAATTATTATATAAG
474723 ATTTTTTAAAATTATTATATAA
1 ATTTTTT-AAATTATTATATAA
474745 CATAGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 3 0.16
22 5 0.26
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTTTTAAATTATTATATAAG
Found at i:478450 original size:182 final size:182
Alignment explanation
Indices: 478063--478536 Score: 707
Period size: 182 Copynumber: 2.6 Consensus size: 182
478053 GATCCAAATT
* * * * **
478063 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACCAGTATTTAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * * *
478128 AAATCGGTAAAGCGGTACCGAATATATTTAAAGTTTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * * *
478193 GTTAATTTAAAAGATAATCAGTTTTAACGCCTATAAAGTGTCGATACTTTCA
131 GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAA
* * *
478245 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
478310 AAACCGGTAAAACGCTACCGGATATATTAAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
478374 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAA
478426 AAAAATGTATCGATCAAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
478491 AAAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
478537 CGTAAGTACG
Statistics
Matches: 262, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 79 0.30
182 183 0.70
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTAA
Found at i:478480 original size:20 final size:19
Alignment explanation
Indices: 478457--478503 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
478447 CGATATAACA
478457 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
478477 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
478497 GGTAAAA
1 GGTAAAA
478504 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:478505 original size:17 final size:19
Alignment explanation
Indices: 478466--478508 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
478456 AGGTAAAAAT
478466 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
478486 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
478503 ATGATA
1 ATGATA
478509 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:480663 original size:15 final size:15
Alignment explanation
Indices: 480643--480675 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
480633 TGGTTGTATT
*
480643 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
480658 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
480673 GGG
1 GGG
480676 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:480855 original size:33 final size:33
Alignment explanation
Indices: 480813--480878 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
480803 AAATAGATGG
*
480813 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
480846 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
480879 TATTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:481104 original size:15 final size:15
Alignment explanation
Indices: 481083--481138 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
481073 AAGAGGGAGG
481083 AGGAAGAAGAAGAGA
1 AGGAAGAAGAAGAGA
*
481098 CGGAAGAA-AAGAGGGA
1 AGGAAGAAGAAGA--GA
481114 GGAGGAAGAAGAAGAGA
1 --AGGAAGAAGAAGAGA
*
481131 TGGAAGAA
1 AGGAAGAA
481139 ATGAGGAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 2 0.06
17 2 0.06
18 7 0.21
19 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.43, T:0.02
Consensus pattern (15 bp):
AGGAAGAAGAAGAGA
Found at i:481105 original size:33 final size:33
Alignment explanation
Indices: 481067--481154 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
481057 AAAATATGAA
481067 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
*
481100 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
*
481133 GAAGAAATGA-GGAGGAAGGAAG
1 GAAGAAAAGAGGGAGG-AGGAAG
481155 TCGATGTCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 5 0.10
33 47 0.90
ACGTcount: A:0.51, C:0.01, G:0.45, T:0.02
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGACG
Found at i:482729 original size:19 final size:20
Alignment explanation
Indices: 482705--482753 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
482695 AATGTAGGGT
482705 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTACGATTTA
482724 TAATTTTGTA-TACGATTTA
1 TAATTTTGTATTACGATTTA
482743 TAATTTTGTAT
1 TAATTTTGTAT
482754 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (20 bp):
TAATTTTGTATTACGATTTA
Found at i:483369 original size:199 final size:200
Alignment explanation
Indices: 482988--483574 Score: 1059
Period size: 199 Copynumber: 2.9 Consensus size: 200
482978 AATTTACAAT
* *
482988 ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
483053 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCAGTATAAGTATACCAGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
483118 ATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
483183 AATGA
196 AATGA
* *
483188 ATGGCAAACAGGGTGTAACCATAAAGTGCCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
483253 TGAAACACATAAGTATAATGTAATAGGTAA-TTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
483317 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
483382 AATGA
196 AATGA
*
483387 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
483452 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACTGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
483517 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
483575 TTTAAATATC
Statistics
Matches: 370, Mismatches: 16, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
199 190 0.51
200 180 0.49
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:485097 original size:18 final size:18
Alignment explanation
Indices: 485074--485110 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
485064 GTGGACAACC
*
485074 AAGCTGTCAATGAAGATG
1 AAGCTGACAATGAAGATG
*
485092 AAGCTGACGATGAAGATG
1 AAGCTGACAATGAAGATG
485110 A
1 A
485111 CGATGAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.30, T:0.19
Consensus pattern (18 bp):
AAGCTGACAATGAAGATG
Found at i:485105 original size:12 final size:12
Alignment explanation
Indices: 485083--485128 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
485073 CAAGCTGTCA
*
485083 ATGAAGATGAAG
1 ATGACGATGAAG
*
485095 CTGACGATGAAG
1 ATGACGATGAAG
485107 ATGACGATGAAG
1 ATGACGATGAAG
*
485119 ATGATGATGA
1 ATGACGATGA
485129 TGATCCAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:485132 original size:6 final size:6
Alignment explanation
Indices: 485083--485128 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
485073 CAAGCTGTCA
* * * *
485083 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
485129 TGATCCAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:486728 original size:185 final size:184
Alignment explanation
Indices: 486414--486763 Score: 594
Period size: 185 Copynumber: 1.9 Consensus size: 184
486404 ATATCAGCAT
* *
486414 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAATATCAGAACCAATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCAGAACCAACAATTATAATGTA
* *
486479 ATAGGTAATTTTGTAATATAACCGATATAGATATACCGGTTTTATGAGAGAATAGGTATACAACC
66 ATAGGTAATTTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTATACAACC
486544 TATATCGACACTTTTTTAATATTGTGTCGC-TACTTTATGTCTAGAATGGATGAAA
131 TATATCGACAC-TTTTTAATATTGTGTC-CATACTTTATGTCTAGAATGGATGAAA
*
486599 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCAGAACCCACAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCAGAACCAACAATTATAATGTA
* * * *
486664 ATAGGTAATTTTTTAATATAATCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTATACAACC
486729 TATATCGACACTTTTTAATATTGTGTCCATACTTT
131 TATATCGACACTTTTTAATATTGTGTCCATACTTT
486764 TAAGTAACGC
Statistics
Matches: 155, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
183 1 0.01
184 22 0.14
185 132 0.85
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCAGAACCAACAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTATACAACC
TATATCGACACTTTTTAATATTGTGTCCATACTTTATGTCTAGAATGGATGAAA
Found at i:490119 original size:182 final size:182
Alignment explanation
Indices: 489462--490482 Score: 1712
Period size: 181 Copynumber: 5.6 Consensus size: 182
489452 TTTTACCTTT
* *
489462 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
489527 AACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
489592 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
489644 TTTAAAAGAGAAG-AGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
489708 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
489773 CGGTTATATTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTAGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
489823 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* *
489887 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* *
489952 CCGGTTATGTTGAAAGTATCGATAATTTATTATAACTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
490005 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
490070 AACAATATAACAGGTAATAATATGATAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
490135 CGATTATGTTGAAAGTGTCGATAA-TTATTATAAGTATCGACACTTTTAGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
490186 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * *
490251 AACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGCAAATCGTTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
490316 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
490368 -TTAATAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAATAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * * **
490432 TAATAATATAACATGTAAAAATATGATAAAATCGGTCTATAAATGACAAAA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
490483 GGTGAACGCA
Statistics
Matches: 792, Mismatches: 40, Indels: 14
0.94 0.05 0.02
Matches are distributed among these distances:
178 4 0.01
179 17 0.02
180 150 0.19
181 326 0.41
182 291 0.37
183 4 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:490665 original size:23 final size:23
Alignment explanation
Indices: 490609--490665 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
490599 TTACTTATAA
*
490609 AATAGGTTAATATAAGCGCTACCT
1 AATACGTT-ATATAAGCGCTACCT
* *
490633 ATTACATTATATAAGCGCTACCT
1 AATACGTTATATAAGCGCTACCT
*
490656 AATATGTTAT
1 AATACGTTAT
490666 TGTACTTGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (23 bp):
AATACGTTATATAAGCGCTACCT
Found at i:490716 original size:87 final size:87
Alignment explanation
Indices: 490618--490780 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
490608 AAATAGGTTA
490618 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
490683 CCGGTTAAATACTTATTTTATT
66 CCGGTTAAATACTTATTTTATT
* * *
490705 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
490770 CCGGTTAAATA
66 CCGGTTAAATA
490781 ATATAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACTTATTTTATT
Found at i:490752 original size:23 final size:23
Alignment explanation
Indices: 490702--490746 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
490692 TACTTATTTT
* *
490702 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
490725 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
490747 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:490885 original size:16 final size:16
Alignment explanation
Indices: 490864--490894 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
490854 AGCGTCGCAT
490864 AGCAGAACTACCCTAC
1 AGCAGAACTACCCTAC
490880 AGCAGAACTACCCTA
1 AGCAGAACTACCCTA
490895 ATGAGAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.35, G:0.13, T:0.13
Consensus pattern (16 bp):
AGCAGAACTACCCTAC
Found at i:502605 original size:31 final size:31
Alignment explanation
Indices: 502569--502645 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
502559 ACAAATTATC
* * **
502569 ATTAAACTTATTGAATTGTTGTAAAATAATT
1 ATTAAACTTATTGAACTATTACAAAATAATT
* **
502600 ATTAAATTTATCAAACTATTACAAAATAATT
1 ATTAAACTTATTGAACTATTACAAAATAATT
*
502631 CTTAAACTTATTGAA
1 ATTAAACTTATTGAA
502646 ATTTATCATT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTAAACTTATTGAACTATTACAAAATAATT
Found at i:503099 original size:32 final size:31
Alignment explanation
Indices: 503063--503140 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 31
503053 CCGACTCCTA
* * * *
503063 ATTTTATATAAATGTACATTTTCTTTAAATTT
1 ATTTTATATAAAT-CACATTATATCTAAATTT
*
503095 ATTTTAATTTAAATCACATTATATCTAAATTT
1 ATTTT-ATATAAATCACATTATATCTAAATTT
*
503127 ATTCTAATATAAAT
1 ATT-TTATATAAAT
503141 ATATTTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 29 0.78
33 8 0.22
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (31 bp):
ATTTTATATAAATCACATTATATCTAAATTT
Found at i:503107 original size:16 final size:16
Alignment explanation
Indices: 503086--503151 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
503076 GTACATTTTC
503086 TTTAAATTTATTTTAA
1 TTTAAATTTATTTTAA
* **
503102 TTTAAA-TCACATTATA
1 TTTAAATTTATTTTA-A
* *
503118 TCTAAATTTATTCTAA
1 TTTAAATTTATTTTAA
* *
503134 TATAAATATATTTTAA
1 TTTAAATTTATTTTAA
503150 TT
1 TT
503152 GTCAATCAAA
Statistics
Matches: 36, Mismatches: 12, Indels: 4
0.69 0.23 0.08
Matches are distributed among these distances:
15 5 0.14
16 27 0.75
17 4 0.11
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTTAA
Found at i:503336 original size:2 final size:2
Alignment explanation
Indices: 503325--503365 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
503315 TTTATATTGT
503325 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
503366 ATGTTTGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:508547 original size:229 final size:227
Alignment explanation
Indices: 508142--508590 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 227
508132 GTAAATTATC
* * *
508142 TATCTTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
508207 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
508272 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
508337 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
* *
508370 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
508435 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
508500 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
508565 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
508591 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
228 39 0.19
229 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:508678 original size:20 final size:19
Alignment explanation
Indices: 508655--508700 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
508645 CGATATACCA
508655 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
508675 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
508695 GGTAAA
1 GGTAAA
508701 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:511136 original size:21 final size:21
Alignment explanation
Indices: 511089--511153 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
511079 AAGACAATCA
* *
511089 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
511111 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
511131 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
511152 AG
1 AG
511154 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:511228 original size:33 final size:33
Alignment explanation
Indices: 511186--511251 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
511176 AAATAGATGG
*
511186 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
511219 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
511252 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:513066 original size:18 final size:19
Alignment explanation
Indices: 513043--513090 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
513033 AATGTAGGGT
513043 TAATTTTGTATAAGA-TTA
1 TAATTTTGTATAAGATTTA
*
513061 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
513080 TATTTTTGTAT
1 TAATTTTGTAT
513091 GTGAATATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:514122 original size:194 final size:197
Alignment explanation
Indices: 513608--514686 Score: 1945
Period size: 195 Copynumber: 5.5 Consensus size: 197
513598 GTGCACCCAT
513608 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
513672 CGGTACAATTATACCGGTTTTATGAGAGAATATGTAT--A-AATGTGTCGACACT-ATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTT
513733 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
513798 TA
196 TA
513800 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
513865 C-GTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAG-TT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTT
* *
513928 -TATCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCAATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
513992 TAA
196 T-A
513995 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
514060 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACT-A-ATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTT
*
514123 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACA-GGTACACCCATAAAGTGTCGATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
514187 TA
196 TA
*
514189 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
514254 CGGTACAATTATACCGGTTTTATGAGAGAATA--TATAAATAATGTGTCGACACTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTT
514317 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
131 GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
514382 TAA
196 T-A
514385 AAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
* * *
514449 CGGTACAATTATATCGATTTTATGAGAGAATATGTCTAAATAATGTGTCGAC-CTAATATAGTTT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTT
514513 GTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
131 GTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATAT
514578 ATA
195 ATA
514581 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
514646 CGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
66 CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAAT
514687 TTATCGATAT
Statistics
Matches: 855, Mismatches: 15, Indels: 29
0.95 0.02 0.03
Matches are distributed among these distances:
192 106 0.12
193 15 0.02
194 207 0.24
195 222 0.26
196 142 0.17
197 163 0.19
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (197 bp):
AAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAATTATACCGGTTTTATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTT
GTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATA
TA
Found at i:514337 original size:390 final size:394
Alignment explanation
Indices: 513194--514678 Score: 2506
Period size: 389 Copynumber: 3.8 Consensus size: 394
513184 CAATATGGCC
* *
513194 AACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAA-CATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
513257 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGGTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
513322 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCAGAATGA
130 GAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTTCCAGAATGA
*
513387 ATGGAAAATAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
194 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCAT
513452 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
258 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
*
513517 TGAGAGAATTTGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
323 TGAGAGAA--TATCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGA
513582 ATGAATGGAA
385 ATGAATGGAA
513592 AACAGGGTG----C----A----C---CC----AT--AAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
513636 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
513700 AATATGTAT--A-AATGTGTCGACACT-ATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
513760 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
513825 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
*
513889 GAGAATATGTCTAAATAATGTGTCGACACTAATATAG-TT-TATCGATATTTTTTTCCAGAATGA
326 GAGAATA--TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
513952 ATGGAA
389 ATGGAA
*
513958 AACAGGGTGCACCCATAAAGTGTCAATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
514023 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
514088 AATATGTATAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
*
514150 GGAAAACA-GGTACACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
*
514214 ACCCAAAAGAATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
*
514279 GAGAATATATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
326 GAGAATATCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
514344 GGAA
391 GGAA
514348 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
514412 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGATTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
514477 AATATGTCTAAATAATGTGTCGAC-CTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
514541 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
196 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
514606 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
514671 GAGAATAT
326 GAGAATAT
514679 GTCTAAATTT
Statistics
Matches: 1034, Mismatches: 17, Indels: 78
0.92 0.02 0.07
Matches are distributed among these distances:
366 31 0.03
367 8 0.01
368 2 0.00
369 56 0.05
370 68 0.07
371 56 0.05
373 18 0.02
374 15 0.01
375 1 0.00
377 48 0.05
378 44 0.04
379 5 0.00
380 2 0.00
381 2 0.00
384 2 0.00
385 2 0.00
387 52 0.05
388 79 0.08
389 197 0.19
390 168 0.16
391 42 0.04
392 127 0.12
395 1 0.00
398 4 0.00
399 4 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (394 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
GAGAATATCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
GGAA
Found at i:516017 original size:18 final size:18
Alignment explanation
Indices: 515996--516057 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
515986 AGCGGTCGCA
515996 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
516014 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
516032 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
516050 GAAGATGA
1 GAAGATGA
516058 TGACGATGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:516020 original size:6 final size:6
Alignment explanation
Indices: 515996--516087 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
515986 AGCGGTCGCA
* * * * * *
515996 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
516044 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
516088 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:516031 original size:3 final size:3
Alignment explanation
Indices: 516011--516091 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
516001 TGAAGCTGAC
* * * * * ** *
516011 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
516059 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
516092 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:516050 original size:36 final size:36
Alignment explanation
Indices: 515999--516075 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
515989 GGTCGCAGAA
*
515999 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* * *
516035 GATGAAGCTGGCGATGAAGATGATGACGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
516071 GATGA
1 GATGA
516076 TGATGAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:516091 original size:12 final size:12
Alignment explanation
Indices: 515999--516087 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
515989 GGTCGCAGAA
*
515999 GATGAAGCTGAC
1 GATGAAGATGAC
516011 GATGAAGATGAC
1 GATGAAGATGAC
*
516023 GATGATGATGAC
1 GATGAAGATGAC
* *
516035 GATGAAGCTGGC
1 GATGAAGATGAC
*
516047 GATGAAGATGAT
1 GATGAAGATGAC
* * *
516059 GACGATGATGAT
1 GATGAAGATGAC
* *
516071 GATGATGATGAA
1 GATGAAGATGAC
516083 GATGA
1 GATGA
516088 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:516091 original size:18 final size:18
Alignment explanation
Indices: 515996--516087 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
515986 AGCGGTCGCA
*
515996 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
516014 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
516032 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
516050 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
516068 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
516086 GA
1 GA
516088 TGATCCAAAC
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:517494 original size:22 final size:22
Alignment explanation
Indices: 517450--517494 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
517440 ATTACATATC
*
517450 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
517472 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATCGAAC-CTT
517494 T
1 T
517495 CAACATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:517831 original size:183 final size:183
Alignment explanation
Indices: 517501--518205 Score: 1256
Period size: 183 Copynumber: 3.9 Consensus size: 183
517491 CTTTCAACAT
*
517501 ATTATAAT-AAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
517565 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTTCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
517630 AATGTGTCAATGCGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
517683 ATTATAATGTAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
517748 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
517813 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* * *
517866 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGCGCGAATA
1 ATTATAATGTAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
517931 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
517996 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATC-GAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
* *
518048 ATTATAATGTAATAGATAATTTTG-TATATAACC-GTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
518111 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* *
518176 AATATGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACGATTTAAAAAAGTGTCG
518206 GTAATTTTAA
Statistics
Matches: 507, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
180 120 0.24
181 8 0.02
182 41 0.08
183 338 0.67
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ATTATAATGTAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:520678 original size:25 final size:25
Alignment explanation
Indices: 520644--520708 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
520634 ATATCATTAA
520644 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
520669 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
* *
520694 ATTTATGTATATACA
1 ATTTAGGTATGTACA
520709 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:521029 original size:21 final size:23
Alignment explanation
Indices: 520982--521029 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
520972 AAATTACATA
520982 ACTTTTAAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAAGTATCGATC
* *
521005 -CTTTT-ATAAAAAGTATGGA-C
1 ACTTTTAAAAAAAAGTATCGATC
521025 ACTTT
1 ACTTT
521030 CAATATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (23 bp):
ACTTTTAAAAAAAAGTATCGATC
Found at i:521077 original size:23 final size:23
Alignment explanation
Indices: 521046--521109 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
521036 ATAGGTAAAC
*
521046 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
521069 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
521092 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
521110 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:521116 original size:23 final size:23
Alignment explanation
Indices: 521046--521118 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
521036 ATAGGTAAAC
* **
521046 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
521069 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
521092 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
521115 ATAT
1 ATAT
521119 TGTAAGTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:521408 original size:24 final size:25
Alignment explanation
Indices: 521376--521439 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
521366 AATTAAACAC
* *
521376 ACATCAATT-AAAATTGTTGTGGGT
1 ACATTAATTGAAAATTGTTATGGGT
*
521400 ACATTAATTGAACATTGTTATGGGT
1 ACATTAATTGAAAATTGTTATGGGT
*
521425 ACATTATTTGGAAAA
1 ACATTAATT-GAAAA
521440 ATAATGTCCG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
24 8 0.24
25 21 0.64
26 4 0.12
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (25 bp):
ACATTAATTGAAAATTGTTATGGGT
Done.