Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006564.1 Hibiscus syriacus cultivar Beakdansim tig00016065_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: 1886890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:364417 original size:24 final size:24
Alignment explanation
Indices: 364390--364457 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
364380 GACATGTCCT
*
364390 TTGATGTTCCAAAAGTTATGCCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
* * *
364414 TTGAAGTTCAAAAAGATATGTCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
*
364438 TTGAAGTGCCAAAAGTTATG
1 TTGAAGTTCCAAAAGTTATG
364458 ATCATCGAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGAAGTTCCAAAAGTTATGCCAC
Found at i:369857 original size:11 final size:11
Alignment explanation
Indices: 369833--369877 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
369823 TATGTGCTGG
369833 AAACAAGATAA
1 AAACAAGATAA
* *
369844 AAATAAGATTA
1 AAACAAGATAA
369855 AAACAAGATAA
1 AAACAAGATAA
369866 AGAA-AAGATAA
1 A-AACAAGATAA
369877 A
1 A
369878 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:369861 original size:22 final size:22
Alignment explanation
Indices: 369833--369874 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
369823 TATGTGCTGG
369833 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
369855 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
369875 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:373639 original size:14 final size:13
Alignment explanation
Indices: 373620--373668 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
373610 AAATTTTGGC
373620 TTTTTTTGCTTTT
1 TTTTTTTGCTTTT
*
373633 TTTTTTTACCTTTT
1 TTTTTTT-GCTTTT
373647 TTTTTTTGCCTTTT
1 TTTTTTTG-CTTTT
373661 TTTGTTTT
1 TTT-TTTT
373669 TTTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 7 0.23
14 20 0.65
15 4 0.13
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTGCTTTT
Found at i:373660 original size:24 final size:22
Alignment explanation
Indices: 373633--373676 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
373623 TTTTGCTTTT
373633 TTTTTTTACCTTTTTTTTTTTGCC
1 TTTTTTT--CTTTTTTTTTTTGCC
*
373657 TTTTTTTGTTTTTTTTTTTG
1 TTTTTTTCTTTTTTTTTTTG
373677 AAAAAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTTTTTGCC
Found at i:374027 original size:11 final size:11
Alignment explanation
Indices: 374003--374047 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
373993 TATATGCTGG
374003 AAACAAGATAA
1 AAACAAGATAA
* *
374014 AAATAAGATTA
1 AAACAAGATAA
374025 AAACAAGATAA
1 AAACAAGATAA
374036 AGAA-AAGATAA
1 A-AACAAGATAA
374047 A
1 A
374048 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:374031 original size:22 final size:22
Alignment explanation
Indices: 374003--374044 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
373993 TATATGCTGG
374003 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
374025 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
374045 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:377812 original size:14 final size:14
Alignment explanation
Indices: 377793--377839 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
377783 CTTTTTTTGC
377793 TTTTTTTGTGCC--
1 TTTTTTTGTGCCTT
*
377805 TTTTTTT-TACCTT
1 TTTTTTTGTGCCTT
*
377818 TTTTTTTTTGCCTT
1 TTTTTTTGTGCCTT
377832 TTTTTTTG
1 TTTTTTTG
377840 CTTTTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 3 0.10
12 7 0.24
13 7 0.24
14 12 0.41
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.77
Consensus pattern (14 bp):
TTTTTTTGTGCCTT
Found at i:377812 original size:25 final size:22
Alignment explanation
Indices: 377784--377846 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 22
377774 AAATTTTGGC
377784 TTTTTTTGCTTTTTTTGTGCCTT
1 TTTTTTTGCTTTTTTT-TGCCTT
**
377807 TTTTTTACCTTTTTTTTTTTGCCTT
1 TTTTTT---TGCTTTTTTTTGCCTT
377832 TTTTTTTGCTTTTTT
1 TTTTTTTGCTTTTTT
377847 GTTTGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 7 0.21
23 6 0.18
25 12 0.36
26 8 0.24
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTTTTGCTTTTTTTTGCCTT
Found at i:377833 original size:11 final size:11
Alignment explanation
Indices: 377784--377846 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 11
377774 AAATTTTGGC
377784 TTTTTTTG-CT
1 TTTTTTTGCCT
377794 TTTTTTGTGCCT
1 TTTTTT-TGCCT
*
377806 TTTTTTTACCTTTT
1 TTTTTTTGCC---T
377820 TTTTTTTGCCTT
1 TTTTTTTGCC-T
377832 TTTTTTTG-CT
1 TTTTTTTGCCT
377842 TTTTT
1 TTTTT
377847 GTTTGAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
10 12 0.26
11 6 0.13
12 18 0.39
14 10 0.22
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:377851 original size:12 final size:12
Alignment explanation
Indices: 377784--377851 Score: 70
Period size: 11 Copynumber: 5.7 Consensus size: 12
377774 AAATTTTGGC
377784 TTTTTTTG-CTT
1 TTTTTTTGCCTT
*
377795 TTTTTGTGCC-T
1 TTTTTTTGCCTT
*
377806 TTTTTTTACCTTTT
1 TTTTTTTGCC--TT
377820 TTTTTTTGCCTT
1 TTTTTTTGCCTT
377832 TTTTTTTG-CTT
1 TTTTTTTGCCTT
377843 TTTTGTTTG
1 TTTT-TTTG
377852 AAAAAATAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
11 23 0.48
12 15 0.31
14 10 0.21
ACGTcount: A:0.01, C:0.12, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTTTTGCCTT
Found at i:380500 original size:19 final size:20
Alignment explanation
Indices: 380476--380526 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
380466 CGGCCAAGAG
* *
380476 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
380495 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
380515 CATGTATTTTCA
1 CATGTATTTTCA
380527 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:387260 original size:35 final size:36
Alignment explanation
Indices: 387213--387280 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
387203 ATTTAGAAGT
387213 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
387248 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
387281 TAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:394352 original size:6 final size:6
Alignment explanation
Indices: 394323--394366 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
394313 AAAAGCAACA
*
394323 AAAAGAG AAAAAG AAAGAAG AAAAAT AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
394367 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:412056 original size:14 final size:14
Alignment explanation
Indices: 412037--412076 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
412027 TAAGATACTA
412037 TTTCCATCACCATC
1 TTTCCATCACCATC
412051 TTTCCATCACCATC
1 TTTCCATCACCATC
*
412065 -CTCCATCACCAT
1 TTTCCATCACCAT
412077 TCACGCCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:412253 original size:15 final size:15
Alignment explanation
Indices: 412233--412268 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
412223 TTTGATATCA
*
412233 TTTCTTGTCATTTCC
1 TTTCTTATCATTTCC
412248 TTTCTTATCATTTCC
1 TTTCTTATCATTTCC
412263 TTTCTT
1 TTTCTT
412269 CTTCCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.25, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTCTTATCATTTCC
Found at i:414512 original size:15 final size:15
Alignment explanation
Indices: 414479--414514 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
414469 AATATGAAAG
*
414479 AAGAAAGGAAATAAT
1 AAGAAAGGAAATAAC
*
414494 AAGAAAGGAAATGAC
1 AAGAAAGGAAATAAC
414509 AAGAAA
1 AAGAAA
414515 TGATATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.22, T:0.08
Consensus pattern (15 bp):
AAGAAAGGAAATAAC
Found at i:414688 original size:13 final size:14
Alignment explanation
Indices: 414670--414705 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
414660 ATGGTCATGA
*
414670 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
414683 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
414697 ATGGTGATG
1 ATGGTGATG
414706 AAAATAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.28, C:0.00, G:0.47, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:414708 original size:13 final size:13
Alignment explanation
Indices: 414670--414708 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
414660 ATGGTCATGA
* *
414670 ATGGTGATGGAGG
1 ATGGTGATGAAAG
414683 ATGGTGATGGAAAG
1 ATGGTGAT-GAAAG
414697 ATGGTGATGAAA
1 ATGGTGATGAAA
414709 ATAGTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:417407 original size:33 final size:33
Alignment explanation
Indices: 417340--417407 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
417330 CAAAAATTAA
*
417340 AAGAAAGAAATGATTAAAATGGAAATATGGAAG
1 AAGAAAGAAATGATTAAAATAGAAATATGGAAG
417373 AAGAAAGGAAATGA-TAAGAA-AGAAA-ATGGCAAG
1 AAGAAA-GAAATGATTAA-AATAGAAATATGG-AAG
417406 AA
1 AA
417408 ATGATATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
32 4 0.13
33 18 0.58
34 9 0.29
ACGTcount: A:0.60, C:0.01, G:0.25, T:0.13
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATAGAAATATGGAAG
Found at i:419240 original size:45 final size:45
Alignment explanation
Indices: 419160--419246 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
419150 AAGACACATT
* * *
419160 CTTTGAATGAAAAATGTTGCCCTTTTGCTGTTCAATGGACACGTC
1 CTTTGAATGAAAAATGTTGCCCATTTACTGCTCAATGGACACGTC
* *
419205 CTTTGAATGAAAAAT-TGTGTCCATTTATTGCTCAATGGACAC
1 CTTTGAATGAAAAATGT-TGCCCATTTACTGCTCAATGGACAC
419247 ATCTTTTGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (45 bp):
CTTTGAATGAAAAATGTTGCCCATTTACTGCTCAATGGACACGTC
Found at i:421921 original size:15 final size:15
Alignment explanation
Indices: 421888--421923 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
421878 AATATGGAAG
*
421888 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAC
*
421903 AAGAAAGGAAATGGC
1 AAGAAAGGAAATGAC
421918 AAGAAA
1 AAGAAA
421924 TGATATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.28, T:0.08
Consensus pattern (15 bp):
AAGAAAGGAAATGAC
Found at i:422456 original size:13 final size:13
Alignment explanation
Indices: 422424--422474 Score: 77
Period size: 13 Copynumber: 3.8 Consensus size: 13
422414 AGATACTATT
422424 TCCATCACCAT-C
1 TCCATCACCATAC
422436 TTTCCATCACCATAC
1 --TCCATCACCATAC
422451 TCCATCACCATAC
1 TCCATCACCATAC
422464 TCCATCACCAT
1 TCCATCACCAT
422475 TCACGCCCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 24 0.67
14 11 0.31
15 1 0.03
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (13 bp):
TCCATCACCATAC
Found at i:422651 original size:15 final size:15
Alignment explanation
Indices: 422631--422666 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
422621 TTTAATATCA
*
422631 TTTCTTGCCATTTCC
1 TTTCTTACCATTTCC
*
422646 TTTCTTATCATTTCC
1 TTTCTTACCATTTCC
422661 TTTCTT
1 TTTCTT
422667 CTTCCATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.28, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTCTTACCATTTCC
Found at i:422873 original size:13 final size:14
Alignment explanation
Indices: 422848--422876 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
422838 AACAAAAAGG
422848 AAAAGAAAGAAGAA
1 AAAAGAAAGAAGAA
422862 AAAAGAAA-AAGAA
1 AAAAGAAAGAAGAA
422875 AA
1 AA
422877 GACTCCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAGAA
Found at i:423073 original size:16 final size:16
Alignment explanation
Indices: 423052--423110 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
423042 GTAAGTTATC
*
423052 TTCATTTTCTTACTAT
1 TTCATTTCCTTACTAT
* *
423068 TTCATTTCCTTATTCT
1 TTCATTTCCTTACTAT
*
423084 TTCATCTT--TTCCTAT
1 TTCAT-TTCCTTACTAT
423099 TTCATTTCCTTA
1 TTCATTTCCTTA
423111 TCTTTTCCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 2 0.06
15 9 0.27
16 20 0.61
17 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTCCTTACTAT
Found at i:426311 original size:14 final size:14
Alignment explanation
Indices: 426292--426333 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
426282 TATAAGATAC
426292 TATTTCCATCACCA
1 TATTTCCATCACCA
426306 TATTTCCATCACCA
1 TATTTCCATCACCA
*
426320 T-TCTCCATCACCA
1 TATTTCCATCACCA
426333 T
1 T
426334 TCACGCCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (14 bp):
TATTTCCATCACCA
Found at i:426328 original size:13 final size:13
Alignment explanation
Indices: 426296--426335 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
426286 AGATACTATT
*
426296 TCCATCACCATATT
1 TCCATCACCAT-TC
426310 TCCATCACCATTC
1 TCCATCACCATTC
426323 TCCATCACCATTC
1 TCCATCACCATTC
426336 ACGCCCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.25, C:0.42, G:0.00, T:0.33
Consensus pattern (13 bp):
TCCATCACCATTC
Found at i:440934 original size:18 final size:18
Alignment explanation
Indices: 440913--440947 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
440903 GGTGAAGTAT
440913 AAATGGTGTTGTCGTGGC
1 AAATGGTGTTGTCGTGGC
440931 AAATGGTGTTGTCGTGG
1 AAATGGTGTTGTCGTGG
440948 TAAGTGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.09, G:0.40, T:0.34
Consensus pattern (18 bp):
AAATGGTGTTGTCGTGGC
Found at i:446004 original size:18 final size:18
Alignment explanation
Indices: 445983--446021 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
445973 TAGTGAAATA
*
445983 TAAATGGCGTTGTCGTCG
1 TAAATGGCATTGTCGTCG
* *
446001 TAAATGGTATTGTCGTGG
1 TAAATGGCATTGTCGTCG
446019 TAA
1 TAA
446022 GTGTTGTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (18 bp):
TAAATGGCATTGTCGTCG
Found at i:453636 original size:34 final size:30
Alignment explanation
Indices: 453592--453685 Score: 129
Period size: 28 Copynumber: 3.0 Consensus size: 30
453582 TTCATCATCC
453592 TATATTAAATTATATTACAAATAATCAATA
1 TATATTAAATTATATTACAAATAATCAATA
453622 TAAATATTGAAAATTATATTACAAATAATC-A-A
1 T--ATATT--AAATTATATTACAAATAATCAATA
453654 TATATTAAATTATATTACAAATAATCACATA
1 TATATTAAATTATATTACAAATAATCA-ATA
453685 T
1 T
453686 TAATCCCGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
28 20 0.35
30 7 0.12
31 2 0.04
32 7 0.12
33 1 0.02
34 20 0.35
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (30 bp):
TATATTAAATTATATTACAAATAATCAATA
Found at i:457900 original size:35 final size:35
Alignment explanation
Indices: 457858--457932 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
457848 CTATCTGTCT
*
457858 ATCACCATCTTCCATCACCATATCACGCCTATATC
1 ATCACCATCTTCCATCACCATATCAAGCCTATATC
*
457893 ATCACCATCTTCCATCACCATTTCAAGCCTATATC
1 ATCACCATCTTCCATCACCATATCAAGCCTATATC
457928 ATCAC
1 ATCAC
457933 TATTCCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.39, G:0.03, T:0.29
Consensus pattern (35 bp):
ATCACCATCTTCCATCACCATATCAAGCCTATATC
Found at i:458444 original size:24 final size:22
Alignment explanation
Indices: 458396--458444 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
458386 CAAACGAAAG
* *
458396 AAAAGAAAAAGAAGAAATTTTC
1 AAAAGAAAAAGAAGAAAGTTGC
458418 AAAAGAAAAAGTGAAGAAAGTTGC
1 AAAAGAAAAA--GAAGAAAGTTGC
458442 AAA
1 AAA
458445 GTACACTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
24 13 0.57
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.14
Consensus pattern (22 bp):
AAAAGAAAAAGAAGAAAGTTGC
Found at i:463566 original size:13 final size:13
Alignment explanation
Indices: 463548--463573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
463538 ATACTATCTG
463548 TCCATCACCATAT
1 TCCATCACCATAT
463561 TCCATCACCATAT
1 TCCATCACCATAT
463574 CACGCCTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (13 bp):
TCCATCACCATAT
Found at i:463605 original size:35 final size:36
Alignment explanation
Indices: 463550--463629 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
463540 ACTATCTGTC
*
463550 CATCACCAT-ATTCCATCACCATATCACGCCTATAT
1 CATCACCATCATTCCACCACCATATCACGCCTATAT
*
463585 CATCACCATCA-TCCACCACCATTTCACGCCTATAT
1 CATCACCATCATTCCACCACCATATCACGCCTATAT
463620 CATCACCATC
1 CATCACCATC
463630 CCTTAACCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 41 0.98
36 1 0.02
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.26
Consensus pattern (36 bp):
CATCACCATCATTCCACCACCATATCACGCCTATAT
Found at i:465643 original size:13 final size:13
Alignment explanation
Indices: 465604--465643 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
465594 CGAGCACTCA
465604 AAAAGAATGAAA-
1 AAAAGAATGAAAG
465616 AAAAG-A--AAAG
1 AAAAGAATGAAAG
465626 AAAAGAATGAAAG
1 AAAAGAATGAAAG
465639 AAAAG
1 AAAAG
465644 TTGAAGCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
9 3 0.12
10 5 0.21
11 2 0.08
12 5 0.21
13 9 0.38
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (13 bp):
AAAAGAATGAAAG
Found at i:469583 original size:25 final size:26
Alignment explanation
Indices: 469546--469597 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
469536 GAAATTTTTG
*
469546 TTTTTTATGTGGAAAAAACAACAAAC
1 TTTTTTATGTGGAAAAAACAAAAAAC
*
469572 TTTTTT-TTTGGAAAAAACAAAAAAC
1 TTTTTTATGTGGAAAAAACAAAAAAC
469597 T
1 T
469598 AACAAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (26 bp):
TTTTTTATGTGGAAAAAACAAAAAAC
Found at i:471228 original size:20 final size:20
Alignment explanation
Indices: 471203--471244 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
471193 CCATGATATG
471203 TAAATGATAT-GAAAACATAA
1 TAAATGA-ATCGAAAACATAA
*
471223 TAAATGAATCTAAAACATAA
1 TAAATGAATCGAAAACATAA
471243 TA
1 TA
471245 TAAAGCTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAATGAATCGAAAACATAA
Found at i:476808 original size:19 final size:18
Alignment explanation
Indices: 476784--476821 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
476774 TCAAGCACTC
476784 AAAAAGAAAAAAAAGGAAA
1 AAAAAGAAAAAAAA-GAAA
*
476803 AAAAAGAAAAGAAAGAAA
1 AAAAAGAAAAAAAAGAAA
476821 A
1 A
476822 GTTAAAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAGAAA
Found at i:476822 original size:9 final size:9
Alignment explanation
Indices: 476784--476821 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
476774 TCAAGCACTC
476784 AAAAAGAAA
1 AAAAAGAAA
476793 AAAAAGGAAA
1 AAAAA-GAAA
476803 AAAAAGAAA
1 AAAAAGAAA
*
476812 AGAAAGAAA
1 AAAAAGAAA
476821 A
1 A
476822 GTTAAAGCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:487219 original size:19 final size:19
Alignment explanation
Indices: 487195--487243 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
487185 AAGCCCCTTT
487195 GAAAATACAT-ATTTTTAAG
1 GAAAATACATGA-TTTTAAG
*
487214 GAAAATACATGATTTTAAT
1 GAAAATACATGATTTTAAG
*
487233 GAATATACATG
1 GAAAATACATG
487244 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (19 bp):
GAAAATACATGATTTTAAG
Found at i:490302 original size:13 final size:13
Alignment explanation
Indices: 490284--490308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
490274 ATAGGCGTGA
490284 ATGGTGATGGAAT
1 ATGGTGATGGAAT
490297 ATGGTGATGGAA
1 ATGGTGATGGAA
490309 AGATAGTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (13 bp):
ATGGTGATGGAAT
Found at i:490834 original size:26 final size:26
Alignment explanation
Indices: 490798--490861 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
490788 ACACGCATGG
490798 CACATGGGTGGCTAGCCATGAGAACT
1 CACATGGGTGGCTAGCCATGAGAACT
*
490824 CACATGGGTGGCTAGCCATGAGCACT
1 CACATGGGTGGCTAGCCATGAGAACT
490850 CACATGGGTGGC
1 CACATGGGTGGC
490862 ATAGGATGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (26 bp):
CACATGGGTGGCTAGCCATGAGAACT
Found at i:499770 original size:11 final size:11
Alignment explanation
Indices: 499756--499787 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
499746 GTTTTAGGAG
499756 TCTTTTCTTTT
1 TCTTTTCTTTT
499767 TCTTTTCTTTT
1 TCTTTTCTTTT
499778 TC-TTTCTTTT
1 TCTTTTCTTTT
499788 GTTTTTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:500042 original size:15 final size:16
Alignment explanation
Indices: 500019--500059 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
500009 GAAATGATAA
500019 GAAAGGAAATGGAAA-T
1 GAAA-GAAATGGAAAGT
500035 GAAAGAAAT-GAAAGT
1 GAAAGAAATGGAAAGT
*
500050 GATAGAAATG
1 GAAAGAAATG
500060 TTATCAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.29, T:0.15
Consensus pattern (16 bp):
GAAAGAAATGGAAAGT
Found at i:500044 original size:9 final size:9
Alignment explanation
Indices: 499989--500048 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
499979 AATATGAAAT
499989 AAGAAATGGA
1 AAGAAAT-GA
*
499999 AAG-AAGGA
1 AAGAAATGA
*
500007 ATGAAATGA
1 AAGAAATGA
*
500016 TAAGAAAGGA
1 -AAGAAATGA
500026 AATGGAAATGA
1 AA--GAAATGA
500037 AAGAAATGA
1 AAGAAATGA
500046 AAG
1 AAG
500049 TGATAGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
8 4 0.10
9 18 0.45
10 10 0.25
11 8 0.20
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (9 bp):
AAGAAATGA
Found at i:500057 original size:35 final size:33
Alignment explanation
Indices: 499991--500057 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
499981 TATGAAATAA
*
499991 GAAATGGAAAGAAGGAATGAAATGATAAGAAAG
1 GAAATGGAAAGAAGAAATGAAATGATAAGAAAG
500024 GAAATGGAAATGAAAGAAATGAAAGTGAT-AGAAA
1 GAAATGGAAA-G-AAGAAATGAAA-TGATAAGAAA
500058 TGTTATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 10 0.33
34 1 0.03
35 15 0.50
36 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.13
Consensus pattern (33 bp):
GAAATGGAAAGAAGAAATGAAATGATAAGAAAG
Found at i:501680 original size:15 final size:15
Alignment explanation
Indices: 501660--501707 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
501650 ATATTTAGTT
501660 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGTG
**
501675 GGGCGGGCGGATACG
1 GGGCGGGCGGATGTG
* *
501690 GGGCAGGAGGATGTG
1 GGGCGGGCGGATGTG
501705 GGG
1 GGG
501708 GCGAGTAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.65, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGTG
Found at i:505454 original size:20 final size:20
Alignment explanation
Indices: 505416--505455 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
505406 GAAAGAAAAT
*
505416 AAAAAGAATAAAATTCAAAG
1 AAAAAGAATAAAATGCAAAG
505436 AAAAAGAA-AAAGATGCAAAG
1 AAAAAGAATAAA-ATGCAAAG
505456 TACACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.70, C:0.05, G:0.15, T:0.10
Consensus pattern (20 bp):
AAAAAGAATAAAATGCAAAG
Found at i:506304 original size:2 final size:2
Alignment explanation
Indices: 506297--506321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
506287 TATGGCAGCG
506297 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
506322 AGTTGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:510015 original size:13 final size:13
Alignment explanation
Indices: 509997--510025 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
509987 AGTTCTTTTA
509997 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
510010 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
510023 TTT
1 TTT
510026 GTTGCAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:510821 original size:19 final size:19
Alignment explanation
Indices: 510797--510833 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
510787 TAAATGATTT
510797 TTTTAATAAAAATACATGA
1 TTTTAATAAAAATACATGA
*
510816 TTTTAATAAAGATACATG
1 TTTTAATAAAAATACATG
510834 CTCTTGCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTTAATAAAAATACATGA
Found at i:512471 original size:90 final size:89
Alignment explanation
Indices: 512329--512491 Score: 254
Period size: 90 Copynumber: 1.8 Consensus size: 89
512319 TTATAGCAAG
* * *
512329 GTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAAATAAATATATATTTAATTAATTGGA
1 GTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAAATAAATATATATTTAATTAATTGAA
*
512394 ATTTAATAATCATATTATATCCAA
66 ATTAAATAATCATATTATATCCAA
* * *
512418 GTTACCCTAATCATATTAGTGATTTTATTATTTCAAATTAATTAAATCTATATTTCATTAATTGA
1 GTTACCCTAATCATATTAG-GATTTTATTATTTCAAATTAAATAAATATATATTTAATTAATTGA
512483 AATTAAATA
65 AATTAAATA
512492 TTCAGGATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
89 19 0.29
90 47 0.71
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (89 bp):
GTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAAATAAATATATATTTAATTAATTGAA
ATTAAATAATCATATTATATCCAA
Found at i:514549 original size:18 final size:18
Alignment explanation
Indices: 514526--514564 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
514516 ACAATGTTCC
514526 CACTAGCCTTCTTATAAA
1 CACTAGCCTTCTTATAAA
514544 CACTAGCCTTCTTATAAA
1 CACTAGCCTTCTTATAAA
514562 CAC
1 CAC
514565 AAGGCTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (18 bp):
CACTAGCCTTCTTATAAA
Found at i:517452 original size:90 final size:89
Alignment explanation
Indices: 517300--517467 Score: 273
Period size: 90 Copynumber: 1.9 Consensus size: 89
517290 ACACACCCTT
* * *
517300 TTATAGCCAAGTTACCCTAATCATATTAGGTTTTTATTATTTTAAATTAGTTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
*
517365 ATTAATTGGAATTTCATAATCCTC
66 ATTAATTGAAATTTCATAATCCTC
* *
517389 TTATATCCAAGTTACCCTAATCATATTTGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATA-TTAGGATTTTATTATTTCAAATTAATTAAATCTATATTT
517454 AATTAATTGAAATT
65 AATTAATTGAAATT
517468 AAATATTTAG
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 24 0.33
90 48 0.67
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTTCATAATCCTC
Found at i:517459 original size:20 final size:20
Alignment explanation
Indices: 517434--517503 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 20
517424 TATTATTTCA
517434 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTATATTT
517454 AATTAATTGAAAT-TAAATATTT
1 AATTAATT-AAATCT--ATATTT
*
517476 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAATC-TATATTT
517498 AATTAA
1 AATTAA
517504 CTCTAGATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
20 12 0.29
21 5 0.12
22 17 0.41
23 3 0.07
24 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTAATTAAATCTATATTT
Found at i:524232 original size:20 final size:20
Alignment explanation
Indices: 524193--524232 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
524183 TATTATTTCA
*
524193 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTAAATTT
524213 AATTAATTGAAAT-TAAATTT
1 AATTAATT-AAATCTAAATTT
524233 TCAGGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTAATTAAATCTAAATTT
Found at i:527588 original size:90 final size:88
Alignment explanation
Indices: 527437--527603 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 88
527427 ATACACCCTT
*
527437 TTATAGCCAAGTTACCAAAATCATATTAGGGTTTTATTATACAAATAAATTAAATCTATATTTAA
1 TTATAGCCAAGTTACCAAAATCATACTAGGGTTTTATTATACAAATAAATTAAATCTATATTTAA
*
527502 TTAATTGGAATTTAATAATCCTC
66 TTAATTGAAATTTAATAATCCTC
* ** * * *
527525 TTATATCCAAGTTACCCTAATTATACTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCAAAATCATACTAGGG-TTTTATTA-TACAAATAAATTAAATCTATATTT
527590 AATTAATTGAAATT
64 AATTAATTGAAATT
527604 AAATTTTCAG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
88 26 0.38
89 8 0.12
90 35 0.51
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.43
Consensus pattern (88 bp):
TTATAGCCAAGTTACCAAAATCATACTAGGGTTTTATTATACAAATAAATTAAATCTATATTTAA
TTAATTGAAATTTAATAATCCTC
Found at i:527609 original size:20 final size:20
Alignment explanation
Indices: 527570--527609 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
527560 TATTATTTCA
*
527570 AATTAATTAAATCTATATTT
1 AATTAATTAAATCTAAATTT
527590 AATTAATTGAAAT-TAAATTT
1 AATTAATT-AAATCTAAATTT
527610 TCAGGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
AATTAATTAAATCTAAATTT
Found at i:534308 original size:75 final size:74
Alignment explanation
Indices: 534175--534318 Score: 252
Period size: 75 Copynumber: 1.9 Consensus size: 74
534165 TAACACACCC
* *
534175 TTTTATAGCCAAGTTACCTTAATCATTTTAGGATTTTATTATTTCAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATT
534240 TAATAATCT
66 TAATAATCT
*
534249 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTA-GGATTTTATTATTTCAAATTAATTAAATCTATAT
534314 TTAAT
65 TTAAT
534319 TAATTGAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
74 27 0.41
75 39 0.59
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (74 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATT
TAATAATCT
Found at i:540591 original size:24 final size:26
Alignment explanation
Indices: 540558--540610 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
540548 TTCAGCAAAG
*
540558 AAATTGAAGCACTC-AAAAGAA-GAA
1 AAATTCAAGCACTCAAAAAGAACGAA
*
540582 AAATTCAAGCTCTCAAAAAGAACGAA
1 AAATTCAAGCACTCAAAAAGAACGAA
540608 AAA
1 AAA
540611 AAAGAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.48
25 7 0.28
26 6 0.24
ACGTcount: A:0.58, C:0.15, G:0.13, T:0.13
Consensus pattern (26 bp):
AAATTCAAGCACTCAAAAAGAACGAA
Found at i:540614 original size:13 final size:13
Alignment explanation
Indices: 540596--540636 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
540586 TCAAGCTCTC
*
540596 AAAAAGAACGAAA
1 AAAAAGAAAGAAA
540609 AAAAAGAAAAGAAA
1 AAAAAG-AAAGAAA
*
540623 AGAAAGAAAGAAA
1 AAAAAGAAAGAAA
540636 A
1 A
540637 GTTGAAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAA
Found at i:547752 original size:46 final size:45
Alignment explanation
Indices: 547627--547762 Score: 175
Period size: 44 Copynumber: 3.0 Consensus size: 45
547617 ATAAAATTTC
* * *
547627 TTATCAATATATTTACCATTTATCCTATAAGCTCGTAAACTTATT
1 TTATCAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATT
* * * *
547672 TTACCAGTATAATTACCA-TTATTCCATAAGCTCGTAAGTTTATT
1 TTATCAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATT
* *
547716 TTATCAATATACTTAACATTTAATCCCATAAGCTCGTAAGCTTATT
1 TTATCAATATAATTACCATTT-ATCCCATAAGCTCGTAAGCTTATT
547762 T
1 T
547763 GCATGGTTAC
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 36 0.47
45 17 0.22
46 23 0.30
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (45 bp):
TTATCAATATAATTACCATTTATCCCATAAGCTCGTAAGCTTATT
Found at i:548662 original size:23 final size:23
Alignment explanation
Indices: 548632--548681 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
548622 AATATAAAAA
548632 ATTCTAGCATTGAATTTATTACC
1 ATTCTAGCATTGAATTTATTACC
548655 ATTCTAGCATTGAATTTATTACC
1 ATTCTAGCATTGAATTTATTACC
548678 ATTC
1 ATTC
548682 AAATGCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (23 bp):
ATTCTAGCATTGAATTTATTACC
Found at i:549924 original size:30 final size:30
Alignment explanation
Indices: 549887--549960 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
549877 TTAAAATTAC
*
549887 ATTTGGTCCCTAAACTTT-TCAAAGTTTATA
1 ATTTGGTCCCTAAACTTTACCAAA-TTTATA
* *
549917 CTTTGGTCACC-AAACTTTACCTAATTTATA
1 ATTTGGTC-CCTAAACTTTACCAAATTTATA
*
549947 ATTTGGTCACTAAA
1 ATTTGGTCCCTAAA
549961 TAAATCCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 1 0.03
30 30 0.83
31 5 0.14
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (30 bp):
ATTTGGTCCCTAAACTTTACCAAATTTATA
Found at i:573217 original size:10 final size:10
Alignment explanation
Indices: 573202--573230 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
573192 GATGTCAAAG
573202 GTAGCTGAAT
1 GTAGCTGAAT
573212 GTAGCTGAAT
1 GTAGCTGAAT
573222 GTAGCTGAA
1 GTAGCTGAA
573231 CATAATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (10 bp):
GTAGCTGAAT
Found at i:590180 original size:15 final size:16
Alignment explanation
Indices: 590146--590197 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
590136 AGGATAAGGT
590146 AATGAAA-AAAGA-AA
1 AATGAAAGAAAGAGAA
*
590160 AGATGAAAGAAA-AGGA
1 A-ATGAAAGAAAGAGAA
*
590176 AATGAAATAAAGAGAA
1 AATGAAAGAAAGAGAA
590192 AATGAA
1 AATGAA
590198 GATAACTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.52
16 14 0.45
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (16 bp):
AATGAAAGAAAGAGAA
Found at i:590834 original size:35 final size:35
Alignment explanation
Indices: 590795--590870 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
590785 ATGATAATGG
* *
590795 GATGGTGATTATATAGGCATGAAATGGAGATGGAA
1 GATGGTGATGATATAGGCATGAAATGGAGATGAAA
* * * *
590830 GATGGTGATGATATATGCGTGATATGGATATGAAA
1 GATGGTGATGATATAGGCATGAAATGGAGATGAAA
590865 GATGGT
1 GATGGT
590871 ATAGATAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (35 bp):
GATGGTGATGATATAGGCATGAAATGGAGATGAAA
Found at i:600340 original size:24 final size:24
Alignment explanation
Indices: 600308--600361 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
600298 TGCAAGGATT
600308 CATTCAAAGGATTTTAAGTTCATC
1 CATTCAAAGGATTTTAAGTTCATC
*
600332 CATTCAAAGGCTTTTAAGTTCATC
1 CATTCAAAGGATTTTAAGTTCATC
600356 CATTCA
1 CATTCA
600362 TGCAAAAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (24 bp):
CATTCAAAGGATTTTAAGTTCATC
Found at i:609709 original size:179 final size:176
Alignment explanation
Indices: 609410--609786 Score: 390
Period size: 180 Copynumber: 2.1 Consensus size: 176
609400 TTGTTTTTAA
* * *
609410 TTATATATTTTAATTATAATGACAAAATGTATAGGCACAAATGATTTTCTCTAATTTTTTGTACA
1 TTATATATTTTAATTATAATGACAAAATATATAGGCACAAATGATTTCCTCCAATTTTTTGTAC-
* * *
609475 AAAAAAATCATATAGTGAAATGTTTTGTAACTATAAGCTATAATTATTGTTACAAAATAAATTAT
65 AAAAAAA-CATATAGTGAAATATTTTGTAACTATAAGCTATAATAATTATTAC-AAA-AAATTAT
* **
609540 CACAATGAATAATGAGATTCAAGTTTTTTAGTAAAAAACAATGTTTGTTG
127 AACAAAAAATAATGAGATTCAAGTTTTTTAGTAAAAAACAATGTTTGTTG
* * * *
609590 TTATATGTTTTAATTATAGTGACAAAATATATTGTCACAAA-GATTTCCCTCCATATTATTTTGT
1 TTATATATTTTAATTATAATGACAAAATATATAGGCACAAATGATTT-CCTCCA-ATT-TTTTGT
* *
609654 GTC-AAAAAA-ATATAGTGACAA-ATTTTGTAACTATAAG-TGTTAATAATTATTACAAAAAATT
63 -ACAAAAAAACATATAGTGA-AATATTTTGTAACTATAAGCT-ATAATAATTATTACAAAAAATT
* * * * ** * *
609715 GTAACAAAAAATAATGATATTCACG-TTTTT-GTGAAAAATTATATTTGTAG
125 ATAACAAAAAATAATGAGATTCAAGTTTTTTAGTAAAAAACAATGTTTGTTG
* *
609765 TTATAAATTTTAACTATAATGA
1 TTATATATTTTAATTATAATGA
609787 TAGCATATAT
Statistics
Matches: 164, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
175 33 0.20
176 5 0.03
177 24 0.15
178 4 0.02
179 40 0.24
180 42 0.26
181 9 0.05
182 6 0.04
183 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (176 bp):
TTATATATTTTAATTATAATGACAAAATATATAGGCACAAATGATTTCCTCCAATTTTTTGTACA
AAAAAACATATAGTGAAATATTTTGTAACTATAAGCTATAATAATTATTACAAAAAATTATAACA
AAAAATAATGAGATTCAAGTTTTTTAGTAAAAAACAATGTTTGTTG
Found at i:611211 original size:3 final size:3
Alignment explanation
Indices: 611203--611267 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
611193 AAGATTATAT
611203 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
611251 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
611268 TTAAGAAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:611514 original size:17 final size:17
Alignment explanation
Indices: 611479--611516 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
611469 CTCTGTTTTA
*
611479 TTTTAAAGAAAATTCAT
1 TTTTAAAGAAAACTCAT
611496 TTTTAAAGAGAAACT-AT
1 TTTTAAAGA-AAACTCAT
611513 TTTT
1 TTTT
611517 TAGTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (17 bp):
TTTTAAAGAAAACTCAT
Found at i:614154 original size:32 final size:32
Alignment explanation
Indices: 614118--614274 Score: 122
Period size: 33 Copynumber: 4.8 Consensus size: 32
614108 TAATATTTTG
*
614118 TCAAAATAAAAAATTATGACAAAT-TTATTTAA
1 TCAAAATAAAAAATTATAACAAATATTATTT-A
* * *
614150 TCAAAATAACAATTTATAACAAATATTAATTTT
1 TCAAAATAAAAAATTATAACAAATATT-ATTTA
** * * * *
614183 TCATTATAAAAAATTGTGACAAATAATATTCTT
1 TCAAAATAAAAAATTATAACAAATATTATT-TA
* *
614216 TCACAATAAAAAATTGTAACAAA-ATTATTTAA
1 TCAAAATAAAAAATTATAACAAATATTATTT-A
* *
614248 TCACAGTAAAAAACTTATAA-AAATATT
1 TCAAAATAAAAAA-TTATAACAAATATT
614275 TAGTGTCGAA
Statistics
Matches: 101, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
31 1 0.01
32 44 0.44
33 52 0.51
34 4 0.04
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (32 bp):
TCAAAATAAAAAATTATAACAAATATTATTTA
Found at i:616751 original size:18 final size:16
Alignment explanation
Indices: 616712--616747 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
616702 TGTAAATAAC
616712 TTAT-ATATATATACA
1 TTATAATATATATACA
616727 TTATAATATATATACA
1 TTATAATATATATACA
616743 TTATA
1 TTATA
616748 TAATCACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATAATATATATACA
Found at i:617476 original size:83 final size:83
Alignment explanation
Indices: 617364--617558 Score: 275
Period size: 83 Copynumber: 2.3 Consensus size: 83
617354 GACATATAAC
*
617364 CCTTCTTGCCTTGAGATATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
617429 TCTTTTGTTGCAAATAGT
66 TCTTTTGTTGCAAATAGT
* * *
617447 CCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGG
1 CCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
* **
617512 TCTTTTGGT-CACATATAAC
66 TCTTTTGTTGCA-A-ATAGT
* * *
617531 CCTTCTAGCCTTGAGTTATGCTGTAAAT
1 CCTTCTTGCCTTGAGATATGCTGCAAAT
617559 TTGACTTGCC
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
82 2 0.02
83 70 0.71
84 27 0.27
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (83 bp):
CCTTCTTGCCTTGAGATATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
TCTTTTGTTGCAAATAGT
Found at i:617748 original size:68 final size:66
Alignment explanation
Indices: 617661--617814 Score: 193
Period size: 66 Copynumber: 2.3 Consensus size: 66
617651 CTAAAAAAAA
* * *
617661 TTTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATCTTGTTTTAAGGGAAATAAAT-TCA
1 TTTG-TGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAAT-AT-TTTCAAGGGAAA-AAATCTCA
617725 AAGAT
62 AAGAT
* * * *
617730 TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATATTTTCAAGGGAAACAATCTCAAAGG
1 TTTGTGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAATATTTTCAAGGGAAAAAATCTCAAAGA
617795 T
66 T
*
617796 TTTGTGTTTCAATAGAAAC
1 TTTGTGTTTCAAGAGAAAC
617815 ATTTTCAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
65 3 0.04
66 36 0.47
67 1 0.01
68 32 0.42
69 4 0.05
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (66 bp):
TTTGTGTTTCAAGAGAAACGGTCTCAAGGGAAACAAAATATTTTCAAGGGAAAAAATCTCAAAGA
T
Found at i:617837 original size:33 final size:33
Alignment explanation
Indices: 617771--617917 Score: 172
Period size: 33 Copynumber: 4.4 Consensus size: 33
617761 GACAAAATAT
* *
617771 TTTCAAGGGAAACAATCTCAAAGG--TTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
* *
617802 TTTCAATAGAAACATTTTCAAAGGTTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
* * *
617835 TTTTAAGAGAAACATTTTCAAAGGATTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
* *
617868 TTTTAATAGAAACAATTTCAAAGGTTTCTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGG--T-TTTTTGTG
617904 TTTCAAGAGAAACA
1 TTTCAAGAGAAACA
617918 GTCTCAAGGG
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
31 20 0.20
33 59 0.60
36 20 0.20
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (33 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTTTTGTG
Found at i:617865 original size:66 final size:66
Alignment explanation
Indices: 617770--617924 Score: 197
Period size: 66 Copynumber: 2.3 Consensus size: 66
617760 AGACAAAATA
* *
617770 TTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAATAGAAACATTTTCAAAGG-T-TTTTTG
1 TTTT-AAGAGAAACAATCTCAAAGGTTTTGTGTTTCAATAGAAACAATTTCAAAGGTTCTTTTTG
617833 TG
65 TG
* * *
617835 TTTTAAGAGAAACATTTTCAAAGGATTTTTGTGTTTTAATAGAAACAATTTCAAAGGTTTCTTTT
1 TTTTAAGAGAAACAATCTCAAAGG--TTTTGTGTTTCAATAGAAACAATTTCAAAGG-TTCTTTT
617900 TGTG
63 TGTG
* *
617904 TTTCAAGAGAAACAGTCTCAA
1 TTTTAAGAGAAACAATCTCAA
617925 GGGAGGCAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
64 17 0.22
65 4 0.05
66 29 0.38
68 1 0.01
69 26 0.34
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (66 bp):
TTTTAAGAGAAACAATCTCAAAGGTTTTGTGTTTCAATAGAAACAATTTCAAAGGTTCTTTTTGT
G
Found at i:618049 original size:36 final size:36
Alignment explanation
Indices: 617987--618144 Score: 230
Period size: 36 Copynumber: 4.4 Consensus size: 36
617977 AAAGAAGCTA
* *
617987 TCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTG
1 TCTCAAGAGAGACTAAA-TTTGTTTCAAGAGAAATTG
*
618024 TCTCAAGAGAGACTAACTTTGTTTCAAG-GTAAATTG
1 TCTCAAGAGAGACTAAATTTGTTTCAAGAG-AAATTG
*
618060 TCTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTG
1 TCTCAAGAGAGACTAAATTTGTTTCAAGAGAAATTG
*
618096 TTTCAAGAGAGACTAAATTTGTTTCAAGAGAAACTT-
1 TCTCAAGAGAGACTAAATTTGTTTCAAGAGAAA-TTG
618132 TCTCAAGAGAGAC
1 TCTCAAGAGAGAC
618145 AATGGTGAGC
Statistics
Matches: 111, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
35 1 0.01
36 93 0.84
37 17 0.15
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
TCTCAAGAGAGACTAAATTTGTTTCAAGAGAAATTG
Found at i:618050 original size:21 final size:21
Alignment explanation
Indices: 617989--618126 Score: 87
Period size: 21 Copynumber: 7.4 Consensus size: 21
617979 AGAAGCTATC
*
617989 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGAC-TAACTTTGTT
*
618011 TCAAG-G-GA--AA--TTGTC
1 TCAAGAGAGACTAACTTTGTT
618026 TCAAGAGAGACTAACTTTGTT
1 TCAAGAGAGACTAACTTTGTT
* *
618047 TC-A-AG-G--TAA-ATTGTC
1 TCAAGAGAGACTAACTTTGTT
*
618062 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGACTAACTTTGTT
618083 TC-A-AGAGA--AAC--TGTT
1 TCAAGAGAGACTAACTTTGTT
*
618098 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGACTAACTTTGTT
618119 TCAAGAGA
1 TCAAGAGA
618127 AACTTTCTCA
Statistics
Matches: 90, Mismatches: 8, Indels: 37
0.67 0.06 0.27
Matches are distributed among these distances:
15 21 0.23
16 6 0.07
17 13 0.14
18 2 0.02
19 11 0.12
20 7 0.08
21 25 0.28
22 5 0.06
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (21 bp):
TCAAGAGAGACTAACTTTGTT
Found at i:618107 original size:72 final size:73
Alignment explanation
Indices: 617970--618146 Score: 243
Period size: 72 Copynumber: 2.4 Consensus size: 73
617960 CAAAGATTGG
* * * * *
617970 TGTTTCAAAAGAAGCTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTTTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
*
618035 ACTAACTT
66 ACTAAATT
* *
618043 TGTTTCAAG-GTAAA-TTGTCTCAAGAGAGACTAAA-TTTGTTTCAAGAGAAACTGTTTCAAGAG
1 TGTTTCAAGAG-AAACTT-TCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
618105 AGACTAAATT
64 AGACTAAATT
618115 TGTTTCAAGAGAAACTTTCTCAAGAGAGACAA
1 TGTTTCAAGAGAAACTTTCTCAAGAGAGACAA
618147 TGGTGAGCAT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
72 62 0.68
73 29 0.32
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTTTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACTAAATT
Found at i:618782 original size:32 final size:32
Alignment explanation
Indices: 618681--618775 Score: 118
Period size: 32 Copynumber: 2.9 Consensus size: 32
618671 ATTCCCAAAG
* * * *
618681 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCAAACATTTGATGTTAAATCTCAAAAA
* *
618713 ATGCCCTAACATTTGATGCTAAATCTCAAAAA
1 ATGCCCAAACATTTGATGTTAAATCTCAAAAA
*
618745 ATGCCCAAACATTTGATGTTTAATCTTCAAA
1 ATGCCCAAACATTTGATGTTAAATC-TCAAA
618776 GATGCCCTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
32 49 0.91
33 5 0.09
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.31
Consensus pattern (32 bp):
ATGCCCAAACATTTGATGTTAAATCTCAAAAA
Found at i:619852 original size:12 final size:13
Alignment explanation
Indices: 619837--619881 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
619827 TTTTCTTCAA
619837 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
619849 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
619861 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
619876 TTTTCT
1 TTTTCT
619882 ATTTTTGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.24
13 14 0.48
14 6 0.21
15 2 0.07
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:619878 original size:26 final size:26
Alignment explanation
Indices: 619836--619887 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
619826 TTTTTCTTCA
*
619836 ATTTTCCTTTG-TTTTTTCTCTTTTT
1 ATTTTCCTTTGCTTTTTTCTATTTTT
619861 ATTTTCTCTTTGCTTTTTTCTATTTTT
1 ATTTTC-CTTTGCTTTTTTCTATTTTT
619888 GTTCTTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (26 bp):
ATTTTCCTTTGCTTTTTTCTATTTTT
Found at i:623157 original size:16 final size:16
Alignment explanation
Indices: 623138--623171 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
623128 TAAAATAAAC
623138 AAAATGAAA-AAAGTAA
1 AAAATGAAATAAA-TAA
623154 AAAATGAAATAAATAA
1 AAAATGAAATAAATAA
623170 AA
1 AA
623172 CATAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAAATGAAATAAATAA
Found at i:624538 original size:20 final size:20
Alignment explanation
Indices: 624513--624552 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
624503 ACTCGGGTTT
624513 GGAGAAACGATGATTGGGCG
1 GGAGAAACGATGATTGGGCG
*
624533 GGAGAAACGATGCTTGGGCG
1 GGAGAAACGATGATTGGGCG
624553 AGAGGATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.12, G:0.45, T:0.15
Consensus pattern (20 bp):
GGAGAAACGATGATTGGGCG
Found at i:624774 original size:16 final size:17
Alignment explanation
Indices: 624750--624788 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
624740 GTAAATAACA
624750 TATATATATATATACAT
1 TATATATATATATACAT
624767 TATA-ATATATATACAT
1 TATATATATATATACAT
624783 TATATA
1 TATATA
624789 ATCACATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATATATATACAT
Found at i:625498 original size:83 final size:84
Alignment explanation
Indices: 625395--625589 Score: 250
Period size: 83 Copynumber: 2.3 Consensus size: 84
625385 TTTTATTGAC
* * *
625395 AGATAACCCTTCTTGCCTTGAGGTTTGCTGTAAATGATGTGCCTTGGAGCTGAACGTAGTCAAAC
1 AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAAC
*
625460 TCGAAGGTATTTTGTTGCA-
66 TCGAAGGTATTTTGGT-CAT
* * * ** *
625479 A-ATAGCCCTTCTTGCCTTGATCTATGTTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAAC
1 AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAAC
*
625543 TCGAAGGTCTTTTGGTCAT
66 TCGAAGGTATTTTGGTCAT
* *
625562 AGATAACCCTTCTAGCCTTGAGTTATGC
1 AGATAACCCTTCTTGCCTTGAGCTATGC
625590 AGTATATTTG
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
82 2 0.02
83 69 0.74
84 22 0.24
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (84 bp):
AGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCAAAC
TCGAAGGTATTTTGGTCAT
Found at i:625912 original size:36 final size:34
Alignment explanation
Indices: 625817--625921 Score: 137
Period size: 33 Copynumber: 3.1 Consensus size: 34
625807 TTTTTCGTGG
*
625817 GAAACAATCTCAAAGG---TTTTGTGTTTCAAGA
1 GAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGA
*
625848 GAAACATTTTCAAAGGTTTTTTT-TGTTTCAAGA
1 GAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGA
*
625881 GAAATAATTTCAAAGGTTTCTTTTTGTGTTTCAAGA
1 GAAACAATTTCAAAGG-TT-TTTTTGTGTTTCAAGA
625917 GAAAC
1 GAAAC
625922 TGTCTTAAGG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
31 14 0.22
33 24 0.38
34 6 0.10
35 5 0.08
36 14 0.22
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.39
Consensus pattern (34 bp):
GAAACAATTTCAAAGGTTTTTTTGTGTTTCAAGA
Found at i:626053 original size:36 final size:36
Alignment explanation
Indices: 625974--626148 Score: 244
Period size: 36 Copynumber: 4.8 Consensus size: 36
625964 CAAAGATTGG
625974 TGTTTCAAGAGAAACTGTCTCAAGAGAGA-TAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACT-AAA-TT
* * * *
626011 TGTTTCAAGGGAAACTATCTCATGAGAGACTAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAATT
* * *
626047 TGTTTCATGGGAAACTGACTCAAGAGAGACTAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAATT
*
626083 TGTTTCAAGAGAAACTGTTTCAAGAGAGACTAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAATT
*
626119 TGTTTCAAGAGACACTGTCTCAAGAGAGAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC
626149 AATGGTGAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
36 93 0.76
37 28 0.23
38 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACTAAATT
Found at i:626092 original size:21 final size:21
Alignment explanation
Indices: 626066--626130 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
626056 GGAAACTGAC
626066 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGACTAAATTTGTT
*
626087 TC-A-AGAG---AAA-CTGTT
1 TCAAGAGAGACTAAATTTGTT
626102 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGACTAAATTTGTT
626123 TCAAGAGA
1 TCAAGAGA
626131 CACTGTCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 6 0.17
16 4 0.11
17 4 0.11
19 4 0.11
20 4 0.11
21 14 0.39
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (21 bp):
TCAAGAGAGACTAAATTTGTT
Found at i:626131 original size:19 final size:19
Alignment explanation
Indices: 626071--626131 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
626061 CTGACTCAAG
626071 AGAGACTAAATTTGTTTCA
1 AGAGACTAAATTTGTTTCA
*
626090 AGAG---AAA-CTGTTTCAA
1 AGAGACTAAATTTGTTTC-A
626106 GAGAGACTAAATTTGTTTCA
1 -AGAGACTAAATTTGTTTCA
626126 AGAGAC
1 AGAGAC
626132 ACTGTCTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 6 0.18
16 4 0.12
17 4 0.12
19 10 0.29
20 4 0.12
21 6 0.18
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (19 bp):
AGAGACTAAATTTGTTTCA
Found at i:627878 original size:14 final size:13
Alignment explanation
Indices: 627836--627884 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
627826 TTTTCTTCAA
627836 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
627848 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
627860 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
627875 TTTTCTCTTT
1 TTTTCTCTTT
627885 TTGTTCTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:627882 original size:27 final size:25
Alignment explanation
Indices: 627835--627886 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
627825 TTTTTCTTCA
627835 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
627860 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
627887 GTTCTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:631057 original size:14 final size:14
Alignment explanation
Indices: 631038--631075 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
631028 AGAAAATAAG
631038 TAAATAAAATAAAC
1 TAAATAAAATAAAC
631052 TAAATAAAATAAAC
1 TAAATAAAATAAAC
*
631066 AAAATGAAAA
1 TAAAT-AAAA
631076 GAGTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAATAAAATAAAC
Found at i:635190 original size:12 final size:12
Alignment explanation
Indices: 635167--635201 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
635157 CTATTTTTTT
635167 CAAAAGAAAAAGG
1 CAAAA-AAAAAGG
*
635180 TAAAAAAAAAGG
1 CAAAAAAAAAGG
635192 CAAAAAAAAA
1 CAAAAAAAAA
635202 ACAAAAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:644337 original size:21 final size:21
Alignment explanation
Indices: 644313--644387 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
644303 TTAAGATTAG
644313 TTTGTGTACTTGGAGTAGTAC
1 TTTGTGTACTTGGAGTAGTAC
* *
644334 TTTGTATACTATGGTAAG-AATAC
1 TTTGTGTACT-TGG--AGTAGTAC
* *
644357 TTAGTGTACTTGTAGTAGTAC
1 TTTGTGTACTTGGAGTAGTAC
644378 TTTGTGTACT
1 TTTGTGTACT
644388 ATGGCACTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.05
21 22 0.51
22 5 0.12
23 12 0.28
24 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44
Consensus pattern (21 bp):
TTTGTGTACTTGGAGTAGTAC
Found at i:654376 original size:35 final size:35
Alignment explanation
Indices: 654334--654426 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 35
654324 TGGATAAGGA
*
654334 ATGGTGATGATATAGGCGTGAAATAGTGATAGAAT
1 ATGGTGATGATATAGGCGTGAAATAGTGATAGAAG
* * *
654369 ATGGTGATGATATAGGCGTGCAATGGTGATTGAAG
1 ATGGTGATGATATAGGCGTGAAATAGTGATAGAAG
654404 ATGGTGATGATATAGGCGTGAAA
1 ATGGTGATGATATAGGCGTGAAA
654427 ATGGTGATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.33, C:0.04, G:0.34, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATAGTGATAGAAG
Found at i:654814 original size:22 final size:20
Alignment explanation
Indices: 654788--654838 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
654778 AGCCCCTTTG
*
654788 AAAATACATGATATTTTTATAA
1 AAAATACATG-TATTTTAAT-A
654810 AAAATACAT-TATTTTAATA
1 AAAATACATGTATTTTAATA
*
654829 AAGATACATG
1 AAAATACATG
654839 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
22 9 0.35
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (20 bp):
AAAATACATGTATTTTAATA
Found at i:654822 original size:20 final size:21
Alignment explanation
Indices: 654788--654830 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
654778 AGCCCCTTTG
*
654788 AAAATACATGATATTTTTATAA
1 AAAATACAT-ATATTTTAATAA
654810 AAAATACAT-TATTTTAATAA
1 AAAATACATATATTTTAATAA
654830 A
1 A
654831 GATACATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAATACATATATTTTAATAA
Found at i:660215 original size:19 final size:20
Alignment explanation
Indices: 660174--660224 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
660164 GAAACCCCTT
*
660174 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTAA
660194 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
660213 TGAAGATACATG
1 TGAAAATACATG
660225 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:668096 original size:54 final size:53
Alignment explanation
Indices: 668053--668337 Score: 183
Period size: 54 Copynumber: 5.3 Consensus size: 53
668043 TTCCATATTT
* * * *
668053 TGCACTCATAGTGCCAAAATGGTTATTTATCCACATGGGATGAATTATGTGAAA
1 TGCACACATAGTGCCAAAATGGTTATTCATCCACATAGGATGAATTATAT-AAA
* * * *
668107 TGCACACTTAGTGCTAAAATGGTTATTCATCCACATAGGATGAATTTTCTGAAA
1 TGCACACATAGTGCCAAAATGGTTATTCATCCACATAGGATGAATTATAT-AAA
* * * *** * * **
668161 TGCACACTTAGTACCGAAACCCTTATTCATCCACATTGGACGAATTCCATGAAA
1 TGCACACATAGTGCCAAAATGGTTATTCATCCACATAGGATGAATTATAT-AAA
* * * * * * * **
668215 TGAAAACTTAGTGACGAAATAGTTATTCATCCACATAGAATGAATTACGTGAAA
1 TGCACACATAGTGCCAAAATGGTTATTCATCCACATAGGATGAATTATAT-AAA
* * * * * * * * *
668269 TGCATACTTGGTGCCGAAACGATTATTCATCCACATAGAATGAATTCTGTGAAA
1 TGCACACATAGTGCCAAAATGGTTATTCATCCACATAGGATGAATTATAT-AAA
* *
668323 TGAACACTTAGTGCC
1 TGCACACATAGTGCC
668338 TATTTGGTAA
Statistics
Matches: 189, Mismatches: 42, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 189 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (53 bp):
TGCACACATAGTGCCAAAATGGTTATTCATCCACATAGGATGAATTATATAAA
Found at i:668187 original size:108 final size:107
Alignment explanation
Indices: 668075--668336 Score: 319
Period size: 108 Copynumber: 2.4 Consensus size: 107
668065 GCCAAAATGG
* * * * *
668075 TTATTTATCCACATGGGATGAATTATGTGAAATGCACACTTAGTGCTAAAATGGTTATTCATCCA
1 TTATTCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGC-AAAATAGTTATTCATCCA
* * *
668140 CATAGGATGAATTTTC-TGAAATGCACACTTAGTACCGAAACCC
65 CATAGAATGAA-TTACGTGAAATGCACACTTAGTACCGAAACCA
* * ** * *
668183 TTATTCATCCACATTGGACGAATTCCATGAAATGAAAACTTAGTGACGAAATAGTTATTCATCCA
1 TTATTCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTG-CAAAATAGTTATTCATCCA
* * * *
668248 CATAGAATGAATTACGTGAAATGCATACTTGGTGCCGAAACGA
65 CATAGAATGAATTACGTGAAATGCACACTTAGTACCGAAACCA
*
668291 TTATTCATCCACATAGAATGAATTCTGTGAAATGAACACTTAGTGC
1 TTATTCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGC
668337 CTATTTGGTA
Statistics
Matches: 129, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
107 4 0.03
108 124 0.96
109 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (107 bp):
TTATTCATCCACATAGGATGAATTCTGTGAAATGAACACTTAGTGCAAAATAGTTATTCATCCAC
ATAGAATGAATTACGTGAAATGCACACTTAGTACCGAAACCA
Found at i:668657 original size:22 final size:21
Alignment explanation
Indices: 668615--668667 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
668605 TGGCTCCTTA
*
668615 GTATCGATAC-ACATACCATG
1 GTATTGATACTACATACCATG
*
668635 GTATTGATACTACTATACTATG
1 GTATTGATACTAC-ATACCATG
*
668657 GTACTGATACT
1 GTATTGATACT
668668 TTGCTATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (21 bp):
GTATTGATACTACATACCATG
Found at i:699565 original size:18 final size:18
Alignment explanation
Indices: 699542--699579 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
699532 ACTCGTAACA
699542 GAATAGAACGTATAATCG
1 GAATAGAACGTATAATCG
699560 GAATAGAACGTATAATCG
1 GAATAGAACGTATAATCG
699578 GA
1 GA
699580 TATAATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (18 bp):
GAATAGAACGTATAATCG
Found at i:699902 original size:15 final size:15
Alignment explanation
Indices: 699878--699916 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
699868 TTTTAAAGAT
* *
699878 TTGAAAGAAAATGAC
1 TTGAATGAAAATGAA
699893 TTGAATGAAAATGAA
1 TTGAATGAAAATGAA
*
699908 TTAAATGAA
1 TTGAATGAA
699917 TTCAAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (15 bp):
TTGAATGAAAATGAA
Found at i:700065 original size:35 final size:35
Alignment explanation
Indices: 700021--700089 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
700011 TCTTTTGATT
*
700021 AAAAGACTTAACTTTTTGACGAAA-TGCTTAACATA
1 AAAAGACTTAA-TTTTTGACGAAAGGGCTTAACATA
* *
700056 AAAAGACTTAATTTTTTATGAAAGGGCTTAACAT
1 AAAAGACTTAATTTTTGACGAAAGGGCTTAACAT
700090 TTTTTTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (35 bp):
AAAAGACTTAATTTTTGACGAAAGGGCTTAACATA
Found at i:700097 original size:23 final size:23
Alignment explanation
Indices: 700056--700118 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
700046 GCTTAACATA
700056 AAAAGACTT-A-A-TTTTTTATG
1 AAAAGACTTAACATTTTTTTATG
* *
700076 AAAGGGCTTAACATTTTTTTATG
1 AAAAGACTTAACATTTTTTTATG
700099 AAAAGACTTAACATTTTTTT
1 AAAAGACTTAACATTTTTTT
700119 CGTGAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 7 0.19
21 1 0.03
22 1 0.03
23 27 0.75
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (23 bp):
AAAAGACTTAACATTTTTTTATG
Found at i:701074 original size:31 final size:31
Alignment explanation
Indices: 701039--701104 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
701029 TTTAAATGTA
*
701039 CAAATTAAATATCTAATAATAAAAATAAATT
1 CAAATTAAATATATAATAATAAAAATAAATT
* * * *
701070 CAAATTAATTTTATTATAATTAAAATAAATT
1 CAAATTAAATATATAATAATAAAAATAAATT
701101 -AAAT
1 CAAAT
701105 AATTTATCAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (31 bp):
CAAATTAAATATATAATAATAAAAATAAATT
Found at i:701111 original size:28 final size:31
Alignment explanation
Indices: 701054--701121 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
701044 TAAATATCTA
* *
701054 ATAATAAAAATAAATTCAAATTAATTTTATT
1 ATAATTAAAATAAATTCAAATTAATTTTATC
701085 ATAATTAAAATAAATT-AAA-TAA-TTTATC
1 ATAATTAAAATAAATTCAAATTAATTTTATC
*
701113 ACAATTAAA
1 ATAATTAAA
701122 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 13 0.38
29 3 0.09
30 3 0.09
31 15 0.44
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (31 bp):
ATAATTAAAATAAATTCAAATTAATTTTATC
Found at i:701204 original size:4 final size:4
Alignment explanation
Indices: 701161--701199 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
701151 TGGGTTAGAA
*
701161 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
701200 TATATCAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:705977 original size:54 final size:54
Alignment explanation
Indices: 705918--706391 Score: 537
Period size: 54 Copynumber: 8.9 Consensus size: 54
705908 GTGTACTATA
*
705918 GGCACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCGTATC
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
** * *
705972 GGCACTATGTGTATAACCCA-CATAATTCATAATGAGTTTGTGAATAACCGTATC
1 GGCACTATGTGTGCAACCCATGA-AATTCATAATGAGTTTGTGAATTACCGTATC
** * * * *
706026 TACACTATATGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACTGTGTC
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
* * * * *
706080 GACACTATGTGTGCAACCCATAAAATTCATAATGAGTTTATGACTTATCGTATC
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
* ** * * *
706134 GCCACTATGTGTG-AACCCAAAAAATTCATAATAAG-TTGTTGAATTACGGTATT
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTG-TGAATTACCGTATC
* * * *
706187 GGCATTATATGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTATCGTATC
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
* * *
706241 GGCACTATGTGTG-AACCCAAGAAATTCATAATGAGTTGGTGAATTACCGTATT
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
* * * *
706294 GGCACTA--TGTGCAACCCACGGAATTCAAAATGAGTTTGTGAATTATCGTATC
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
* * * ** *
706346 GACACTATATGTGCAACCCATGGAATTCATAACAAGTTTGTTAATT
1 GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATT
706392 TCCATATCAA
Statistics
Matches: 352, Mismatches: 60, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
51 4 0.01
52 42 0.12
53 82 0.23
54 220 0.62
55 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
GGCACTATGTGTGCAACCCATGAAATTCATAATGAGTTTGTGAATTACCGTATC
Found at i:706109 original size:108 final size:108
Alignment explanation
Indices: 705920--706391 Score: 567
Period size: 107 Copynumber: 4.4 Consensus size: 108
705910 GTACTATAGG
* * *
705920 CACTATGTGTGCAACCCATGGAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTA
1 CACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTG
* * * * *
705985 TAACCCACATAATTCATAATGAGTTTGTGAATAACCGTATCTA
66 CAACCCACAGAATTCATAATGAGTTTGTGAATTATCGTATCGA
* * * * *
706028 CACTATATGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACTGTGTCGACACTATGTGTG
1 CACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTG
* * * * *
706093 CAACCCATAAAATTCATAATGAGTTTATGACTTATCGTATCGC
66 CAACCCACAGAATTCATAATGAGTTTGTGAATTATCGTATCGA
* * * * * *
706136 CACTATGTGTG-AACCCAAAAAATTCATAATAAG-TTGTTGAATTACGGTATTGGCATTATATGT
1 CACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTG-TGAATTACCGTATCGGCACTATGTGT
** *
706199 GCAACCCATGGAATTCATAATGAGTTTGTGAATTATCGTATCGG
65 GCAACCCACAGAATTCATAATGAGTTTGTGAATTATCGTATCGA
* *
706243 CACTATGTGTG-AACCCAAGAAATTCATAATGAGTTGGTGAATTACCGTATTGGCACTA--TGTG
1 CACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTG
* *
706305 CAACCCACGGAATTCAAAATGAGTTTGTGAATTATCGTATCGA
66 CAACCCACAGAATTCATAATGAGTTTGTGAATTATCGTATCGA
* * * ** *
706348 CACTATATGTGCAACCCATGGAATTCATAACAAGTTTGTTAATT
1 CACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTGTGAATT
706392 TCCATATCAA
Statistics
Matches: 315, Mismatches: 46, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
105 54 0.17
106 29 0.09
107 128 0.41
108 104 0.33
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (108 bp):
CACTATGTGTGCAACCCAAGAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTG
CAACCCACAGAATTCATAATGAGTTTGTGAATTATCGTATCGA
Found at i:708138 original size:18 final size:18
Alignment explanation
Indices: 708117--708151 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
708107 GTTTCCACAG
708117 TGGTGAAACTGGCCACTC
1 TGGTGAAACTGGCCACTC
* *
708135 TGGTGAAGCTGGTCACT
1 TGGTGAAACTGGCCACT
708152 ATACTCGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
TGGTGAAACTGGCCACTC
Found at i:712351 original size:20 final size:21
Alignment explanation
Indices: 712298--712354 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
712288 ATACCGAAGT
*
712298 GGGTATCGATACCATAGAAGAG
1 GGGTATCGATACTATAG-AGAG
** *
712320 AAGTATCAATACTATAG-GAG
1 GGGTATCGATACTATAGAGAG
712340 GGGTATCGATACTAT
1 GGGTATCGATACTAT
712355 TCAGTCTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.54
22 13 0.46
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (21 bp):
GGGTATCGATACTATAGAGAG
Found at i:712658 original size:54 final size:54
Alignment explanation
Indices: 712576--712792 Score: 281
Period size: 54 Copynumber: 4.0 Consensus size: 54
712566 CTATATGCAA
712576 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
1 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * * * *
712630 TATGTGTGCAACCCACAGAATTCATAATGAGTTTATGAATTACTGTTTCAGCAC
1 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
* * *
712684 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTATCGTTTCGGTAC
1 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
** *** * * * *
712738 TAAATGTGCAACCCATGGAATTCATAATGTGTTTGTGAATTTCCATATGGGCAC
1 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
712792 T
1 T
712793 TAGGTGCAAA
Statistics
Matches: 140, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 140 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (54 bp):
TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCAC
Found at i:712765 original size:108 final size:108
Alignment explanation
Indices: 712576--712778 Score: 325
Period size: 108 Copynumber: 1.9 Consensus size: 108
712566 CTATATGCAA
**
712576 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTATGTGTGCAA
1 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTAAATGTGCAA
712641 CCCACAGAATTCATAATGAGTTTATGAATTACTGTTTCAGCAC
66 CCCACAGAATTCATAATGAGTTTATGAATTACTGTTTCAGCAC
* * *
712684 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTATCGTTTCGGTACTAAATGTGCAA
1 TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTAAATGTGCAA
** * *
712749 CCCATGGAATTCATAATGTGTTTGTGAATT
66 CCCACAGAATTCATAATGAGTTTATGAATT
712779 TCCATATGGG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 86 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (108 bp):
TATGTGTGCAACCCACAAAATTCATAATGAGTTTGTGAATTACCGTATCGGCACTAAATGTGCAA
CCCACAGAATTCATAATGAGTTTATGAATTACTGTTTCAGCAC
Found at i:714851 original size:17 final size:17
Alignment explanation
Indices: 714831--714900 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
714821 CTAGTTTGAG
*
714831 TAGTTTAATGAATGAAG
1 TAGTTTAATGAATGAAC
* *
714848 TAGTTTGATTAATGAAC
1 TAGTTTAATGAATGAAC
*
714865 TAATTTAATGAATGAAC
1 TAGTTTAATGAATGAAC
*
714882 TAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
714899 TA
1 TA
714901 ACTTTATGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:714872 original size:34 final size:35
Alignment explanation
Indices: 714834--714916 Score: 116
Period size: 34 Copynumber: 2.4 Consensus size: 35
714824 GTTTGAGTAG
* * *
714834 TTTAATGAATGAAGTAGTTTGATTAATGAACTAA-
1 TTTAATGAATGAACTAGTTTAATCAATGAACTAAC
714868 TTTAATGAATGAACTAGTTTAATCAATGAACTAAC
1 TTTAATGAATGAACTAGTTTAATCAATGAACTAAC
714903 TTT-ATGTAATGAAC
1 TTTAATG-AATGAAC
714917 ATGCTGACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 34 0.77
35 10 0.23
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (35 bp):
TTTAATGAATGAACTAGTTTAATCAATGAACTAAC
Found at i:719905 original size:23 final size:23
Alignment explanation
Indices: 719875--719923 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
719865 CAACTTAAAC
719875 AAACTCGGTTAGGTAGTAGTTTG
1 AAACTCGGTTAGGTAGTAGTTTG
719898 AAACTCGGTTAGGTAGTAGTTTG
1 AAACTCGGTTAGGTAGTAGTTTG
719921 AAA
1 AAA
719924 TAAGTAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.33
Consensus pattern (23 bp):
AAACTCGGTTAGGTAGTAGTTTG
Done.