Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005805.1 Hibiscus syriacus cultivar Beakdansim tig00013613_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: 136867
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:497 original size:20 final size:20
Alignment explanation
Indices: 472--561 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
462 GCTATGTAAA
*
472 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTAAGTAT
*
492 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTAAGTAT
**
512 TCGCATTGCGATTT-TCTAAT
1 TCGCATTGCGATTTAAGT-AT
*
532 TCGCATTGCGA-TTACGTAT
1 TCGCATTGCGATTTAAGTAT
551 TCGCATTGCGA
1 TCGCATTGCGA
562 ATTATGAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
19 19 0.31
20 42 0.69
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTAAGTAT
Found at i:534 original size:40 final size:39
Alignment explanation
Indices: 471--703 Score: 161
Period size: 40 Copynumber: 5.8 Consensus size: 39
461 CGCTATGTAA
**
471 ATCGCATTGCGATAGT-AAGATTCGCATTGCGATTTACGT
1 ATCGCATTGCGATTTTCAA-ATTCGCATTGCGATTTACGT
*
510 ATTCGCATTGCGATTTTCTAATTCGCATTGCGA-TTACGT
1 A-TCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGT
* * * ** *
549 ATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGT
1 A-TCGCATTGCG-ATTTTCAAATTCGCATTGCGATTTACGT
* *** *
589 AAATCGCAATGCGAATTAGGAAAATT-GCATTGCGATAGT-CAGT
1 --ATCGCATTGCG-ATT-TTCAAATTCGCATTGCGAT-TTAC-GT
* *
632 ATCGCATTGCGATTTTCCAAATTCGTATTGCGATTTACTT
1 ATCGCATTGCGATTTT-CAAATTCGCATTGCGATTTACGT
* **
672 ATCGCATTGCGATTTACTTATTCGCATTGCGA
1 ATCGCATTGCGATTTTCAAATTCGCATTGCGA
704 ATTGGGAAAA
Statistics
Matches: 153, Mismatches: 29, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
39 32 0.21
40 71 0.46
41 41 0.27
42 6 0.04
43 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (39 bp):
ATCGCATTGCGATTTTCAAATTCGCATTGCGATTTACGT
Found at i:582 original size:21 final size:21
Alignment explanation
Indices: 558--613 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
548 TATTCGCATT
*
558 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
579 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
599 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
614 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:622 original size:21 final size:21
Alignment explanation
Indices: 551--623 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
541 GATTACGTAT
* *
551 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
572 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
592 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
613 TTGCATTGCGA
1 TCGCAATGCGA
624 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:698 original size:20 final size:20
Alignment explanation
Indices: 633--703 Score: 90
Period size: 19 Copynumber: 3.5 Consensus size: 20
623 ATAGTCAGTA
* **
633 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACTTAT
*
654 TCGTATTGCGATTTACTTA-
1 TCGCATTGCGATTTACTTAT
673 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
693 TCGCATTGCGA
1 TCGCATTGCGA
704 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 18 0.41
20 16 0.36
21 10 0.23
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:725 original size:122 final size:120
Alignment explanation
Indices: 512--751 Score: 288
Period size: 122 Copynumber: 2.0 Consensus size: 120
502 ATTTACGTAT
*
512 TCGCATTGCGATTTTCTAATTCGCATTGCGATTACGTATTCGCATTGCGAATTATGAAAATCGCA
1 TCGCATTGCGATTTTCAAATTCGCATTGCGATTACGTATTCGCATTGCGAATTAT-AAAATCGCA
* * *
577 ACGCGAATACGTAAATCGCAATGCG-AATTAGGAAAATTGCATTGCGATAGTCAGTA
65 ACGCGAATACGAAAATCGCAACGCGAAATT-GGAAAATCGCATTGCGATAGTCAGTA
* * * * *
633 TCGCATTGCGATTTTCCAAATTCGTATTGCGATTTACTTA-TCGCATTGCGATTTACT-TATTCG
1 TCGCATTGCGATTTT-CAAATTCGCATTGCGA-TTACGTATTCGCATTGCGAATTA-TAAAATCG
** **
696 CATTGCGAATTGGGAAAATCGCAACGCGAAATTGGAAAATCGCATTGCGATAGTCA
63 CAACGCGAA-TACGAAAATCGCAACGCGAAATTGGAAAATCGCATTGCGATAGTCA
752 TAATCGGTTG
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
121 26 0.26
122 64 0.63
123 11 0.11
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (120 bp):
TCGCATTGCGATTTTCAAATTCGCATTGCGATTACGTATTCGCATTGCGAATTATAAAATCGCAA
CGCGAATACGAAAATCGCAACGCGAAATTGGAAAATCGCATTGCGATAGTCAGTA
Found at i:745 original size:21 final size:22
Alignment explanation
Indices: 693--745 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
683 ATTTACTTAT
693 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
714 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
735 TCGCATTGCGA
1 TCGCATTGCGA
746 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1227 original size:20 final size:20
Alignment explanation
Indices: 1194--1231 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1184 ATATTGAGAA
1194 TAATATTATCGGAATATGTAT
1 TAATATTATCGGAA-ATGTAT
*
1215 TAAT-TTATTGGAAATGT
1 TAATATTATCGGAAATGT
1232 TATATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (20 bp):
TAATATTATCGGAAATGTAT
Found at i:1575 original size:11 final size:11
Alignment explanation
Indices: 1554--1584 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1544 TCCTGCAAAG
1554 GAGACCCATGTT
1 GAGA-CCATGTT
1566 GAGACCATGTT
1 GAGACCATGTT
1577 GAGACCAT
1 GAGACCAT
1585 CGAGTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (11 bp):
GAGACCATGTT
Found at i:4000 original size:18 final size:18
Alignment explanation
Indices: 3958--4029 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
3948 GCCGGTTCCA
* *
3958 ACCCGACCCCGTTTACCCA
1 ACCCGA-CCCGTTGACCCG
* * *
3977 ATCCGACCTGTTTACCCG
1 ACCCGACCCGTTGACCCG
*
3995 ACCCGACCCATTGACCCG
1 ACCCGACCCGTTGACCCG
*
4013 ACCCGACCTGTTGACCC
1 ACCCGACCCGTTGACCC
4030 TATGACCGGC
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 39 0.89
19 5 0.11
ACGTcount: A:0.19, C:0.47, G:0.15, T:0.18
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:6860 original size:62 final size:63
Alignment explanation
Indices: 6789--6911 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 63
6779 CTAATATGAC
* * * *
6789 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-AT-TTCGGGTAGGCCCT-ACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTT-GGGTAGGCCCTCA-GGCCCTAAGATGTGT
*
6851 TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTTGGGTAGGCCCTCAGGCCCTAAGATGT
6912 TCCCTTAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 25 0.47
63 25 0.47
64 3 0.06
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCTACGGCCCCGAAATCTATCTTGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:6919 original size:63 final size:62
Alignment explanation
Indices: 6790--6921 Score: 153
Period size: 63 Copynumber: 2.1 Consensus size: 62
6780 TAATATGACT
* * * * *
6790 CTTAGGTAGGCTCTGCGGCCCTGAGATCATTTCGGGTAGGCCCTACGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCCTACGGCCCCGAAATCATTTCGGGTAGGCCCTACGGCCCTAAGATGTGTC
*
6852 CTTAGGTAGGCCCTACGGCCCCGAAATCTATCTT-GGGTAGGCTCT-CAGGCCCTAAGATGT-TC
1 CTTAGGTAGGCCCTACGGCCCCGAAATC-AT-TTCGGGTAGGCCCTAC-GGCCCTAAGATGTGT-
6914 C
62 C
6915 CTTAGGT
1 CTTAGGT
6922 TAACTCTTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
62 26 0.43
63 32 0.53
64 2 0.03
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.27
Consensus pattern (62 bp):
CTTAGGTAGGCCCTACGGCCCCGAAATCATTTCGGGTAGGCCCTACGGCCCTAAGATGTGTC
Found at i:7679 original size:20 final size:20
Alignment explanation
Indices: 7656--7778 Score: 59
Period size: 20 Copynumber: 5.9 Consensus size: 20
7646 AACAGTTTCC
7656 GAATTCGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
* * ** *
7676 GAATTCGTAACAC-ATAAGTA
1 GAATTCGCAACTCGA-ATTTG
* **
7696 GAATTCGCAACTTGAACATG
1 GAATTCGCAACTCGAATTTG
* *
7716 GAAATTTTCGCAACACGAATTTC
1 G-AA--TTCGCAACTCGAATTTG
** *
7739 GTTTTCGCAACTCGAATTCG
1 GAATTCGCAACTCGAATTTG
*
7759 CAAATTTCGCAACTCGAATT
1 -GAA-TTCGCAACTCGAATT
7779 CGCCAATTTT
Statistics
Matches: 72, Mismatches: 24, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
19 1 0.01
20 40 0.56
21 3 0.04
22 15 0.21
23 13 0.18
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (20 bp):
GAATTCGCAACTCGAATTTG
Found at i:7795 original size:22 final size:22
Alignment explanation
Indices: 7741--7787 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
7731 CGAATTTCGT
7741 TTTCGCAACTCGAATTCGCAAA
1 TTTCGCAACTCGAATTCGCAAA
*
7763 TTTCGCAACTCGAATTCGCCAA
1 TTTCGCAACTCGAATTCGCAAA
7785 TTT
1 TTT
7788 TGTAACTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (22 bp):
TTTCGCAACTCGAATTCGCAAA
Found at i:7902 original size:96 final size:97
Alignment explanation
Indices: 7772--7972 Score: 289
Period size: 96 Copynumber: 2.1 Consensus size: 97
7762 ATTTCGCAAC
* * * * *
7772 TCGAATTCGCCAATTTTGTAACTCAATTACCGATATAGGTAAACATGGTA-AAAAATCTGGTAAA
1 TCGAATTTGCCAATTTTGCAACTCAATTACCGATATAGGTAAACACGATAGAAAAATCTGATAAA
* *
7836 AAACCCGAATTCGCCAATTTGAAAACTGAG-T
66 AAACCCGAATTCGCCAAATTGAAAACTAAGTT
*
7867 TCGAATTTGACCAATTTTGCAACTCAATTACCGATATAGGTAAACACGATAGAAAAATCTGATAT
1 TCGAATTTG-CCAATTTTGCAACTCAATTACCGATATAGGTAAACACGATAGAAAAATCTGATAA
**
7932 AAAATTCGAATTCGCCAAATTGAAAACTAAGTT
65 AAAACCCGAATTCGCCAAATTGAAAACTAAGTT
7965 TCGAATTT
1 TCGAATTT
7973 CGCAAATTCG
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 8 0.09
96 38 0.41
97 38 0.41
98 9 0.10
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (97 bp):
TCGAATTTGCCAATTTTGCAACTCAATTACCGATATAGGTAAACACGATAGAAAAATCTGATAAA
AAACCCGAATTCGCCAAATTGAAAACTAAGTT
Found at i:9283 original size:25 final size:25
Alignment explanation
Indices: 9254--9302 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
9244 GTTACGAATT
9254 CATTGACTTGTTTTAATGAATTTTG
1 CATTGACTTGTTTTAATGAATTTTG
* *
9279 CATTGACTTGTTTTAGTTAATTTT
1 CATTGACTTGTTTTAATGAATTTT
9303 TACATAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.55
Consensus pattern (25 bp):
CATTGACTTGTTTTAATGAATTTTG
Found at i:14257 original size:17 final size:17
Alignment explanation
Indices: 14201--14259 Score: 52
Period size: 20 Copynumber: 3.4 Consensus size: 17
14191 ATTCTTCTAT
*
14201 TTTATTTATTTT-CTCA
1 TTTATTTATTTTATTCA
14217 -TTA-TTATTTTTATTCAA
1 TTTATTTA-TTTTATTC-A
14234 TAATTATTTATTTTATTCA
1 T--TTATTTATTTTATTCA
14253 TTTATTT
1 TTTATTT
14260 TCATTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
14 3 0.09
15 7 0.20
16 2 0.06
17 7 0.20
19 2 0.06
20 11 0.31
21 3 0.09
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTATTTTATTCA
Found at i:16729 original size:13 final size:13
Alignment explanation
Indices: 16713--16745 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16703 CATATCGACC
*
16713 TTTCTTTCTTTAT
1 TTTCTTTCATTAT
16726 TTTCTTTCATTAT
1 TTTCTTTCATTAT
16739 TTTCTTT
1 TTTCTTT
16746 TCACAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCATTAT
Found at i:17535 original size:24 final size:25
Alignment explanation
Indices: 17496--17557 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
17486 ACTTTATTTA
17496 TTTA-TTG-AAAATTAAGAATTATT
1 TTTATTTGAAAAATTAAGAATTATT
17519 TTTATTT-AAAAATTAAGAATTATT
1 TTTATTTGAAAAATTAAGAATTATT
17543 TTTATTTGAAAAATT
1 TTTATTTGAAAAATT
17558 CGATGCTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
23 4 0.11
24 25 0.69
25 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
TTTATTTGAAAAATTAAGAATTATT
Found at i:18010 original size:14 final size:14
Alignment explanation
Indices: 17991--18020 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17981 CCAATCAATT
*
17991 AATGAATGCATTTG
1 AATGAATGCATCTG
18005 AATGAATGCATCTG
1 AATGAATGCATCTG
18019 AA
1 AA
18021 AAGGAAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (14 bp):
AATGAATGCATCTG
Found at i:20215 original size:22 final size:23
Alignment explanation
Indices: 20180--20226 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
20170 CCGTGTTTGG
20180 TTCGTTTAATATTCGTGAACATA
1 TTCGTTTAATATTCGTGAACATA
*
20203 TTCGTTTAA-ATTCGTGAATATA
1 TTCGTTTAATATTCGTGAACATA
20225 TT
1 TT
20227 GTATATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (23 bp):
TTCGTTTAATATTCGTGAACATA
Found at i:20464 original size:99 final size:101
Alignment explanation
Indices: 20321--20521 Score: 379
Period size: 99 Copynumber: 2.0 Consensus size: 101
20311 TTAGTCCTTA
20321 ATTTTTATTGTCTTCACAGCTTGAACTTCAAAGTTCATCTTATGTTCAATTTAGTATGTACTTTC
1 ATTTTTATTGTCTTCACAGCTTGAACTTCAAAGTTCATCTTATGTTCAATTTAGTATGTACTTTC
*
20386 AC-T-TATTTAAAAGAGGAGAGAGAGAGAGATAGAG
66 ACTTATATTTAAAAGAGGAGAGAGAGAGAGAGAGAG
20420 ATTTTTATTGTCTTCACAGCTTGAACTTCAAAGTTCATCTTATGTTCAATTTAGTATGTACTTTC
1 ATTTTTATTGTCTTCACAGCTTGAACTTCAAAGTTCATCTTATGTTCAATTTAGTATGTACTTTC
20485 ACTTATATTTAAAAGAGGAGAGAGAGAGAGAGAGAG
66 ACTTATATTTAAAAGAGGAGAGAGAGAGAGAGAGAG
20521 A
1 A
20522 GAAAGAATCG
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
99 67 0.68
100 1 0.01
101 31 0.31
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (101 bp):
ATTTTTATTGTCTTCACAGCTTGAACTTCAAAGTTCATCTTATGTTCAATTTAGTATGTACTTTC
ACTTATATTTAAAAGAGGAGAGAGAGAGAGAGAGAG
Found at i:21393 original size:15 final size:16
Alignment explanation
Indices: 21373--21411 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
21363 CTGCACCAAG
*
21373 AAAATAAAC-AAAGCC
1 AAAATAAACTAAAGCA
*
21388 AAAATAAACTAAAGTA
1 AAAATAAACTAAAGCA
21404 AAAATAAA
1 AAAATAAA
21412 ATTGAAACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.13
Consensus pattern (16 bp):
AAAATAAACTAAAGCA
Found at i:24481 original size:40 final size:39
Alignment explanation
Indices: 24423--24542 Score: 197
Period size: 40 Copynumber: 3.1 Consensus size: 39
24413 TGCAGGTTTA
*
24423 TAATACACTTCGGTGTATATGGTGGACACGACCTTATGTG
1 TAATACACTTCGG-GTATATGGTGGGCACGACCTTATGTG
24463 TAATACACTTCGGAGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGG-GTATATGGTGGGCACGACCTTATGTG
*
24503 TAATACACTTC-GGTGTATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGGTATATGGTGGGCACGACCTTATGTG
24541 TA
1 TA
24543 GCACTACGGT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 27 0.35
39 1 0.01
40 49 0.64
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (39 bp):
TAATACACTTCGGGTATATGGTGGGCACGACCTTATGTG
Found at i:24741 original size:47 final size:45
Alignment explanation
Indices: 24647--24772 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
24637 GTAACCATGC
* * *
24647 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
24691 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
24738 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
24773 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:26281 original size:13 final size:13
Alignment explanation
Indices: 26263--26292 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
26253 AGAAGAAAAA
26263 AAAATAGAAAATG
1 AAAATAGAAAATG
26276 AAAATAGAAAATG
1 AAAATAGAAAATG
26289 AAAA
1 AAAA
26293 CGAAAACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATAGAAAATG
Found at i:30184 original size:40 final size:40
Alignment explanation
Indices: 30129--30250 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
30119 TGCAGGTTTA
30129 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
30169 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
30209 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
30249 TA
1 TA
30251 GCACTACGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:30449 original size:47 final size:45
Alignment explanation
Indices: 30355--30480 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
30345 GTAACCATGC
* * *
30355 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
30399 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
* *
30446 AAATAAGTTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
30481 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:39795 original size:35 final size:37
Alignment explanation
Indices: 39731--39805 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 37
39721 TTTCGTCATA
39731 CTAGGATTCAAACTCACAAAAATAAGATAGAATTCTG
1 CTAGGATTCAAACTCACAAAAATAAGATAGAATTCTG
** * *
39768 CTAGGATTC-AACTC-TTAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCACAAAAATAAGATAGAATTCTG
39803 CTA
1 CTA
39806 TGTTTTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 20 0.59
36 5 0.15
37 9 0.26
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCACAAAAATAAGATAGAATTCTG
Found at i:40292 original size:11 final size:11
Alignment explanation
Indices: 40272--40352 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
40262 TTAATTATTT
*
40272 TTATTCTAATA
1 TTATTTTAATA
*
40283 TTATTTTAATG
1 TTATTTTAATA
40294 TT-TTTTAA-A
1 TTATTTTAATA
*
40303 GTTATTAT-ATA
1 -TTATTTTAATA
*
40314 TATATTATAACTA
1 T-TATTTTAA-TA
*
40327 TTATATTTATTA
1 TTAT-TTTAATA
*
40339 TTATTTTACTA
1 TTATTTTAATA
40350 TTA
1 TTA
40353 ACGTATATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 10 0.18
11 30 0.54
12 10 0.18
13 6 0.11
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:40535 original size:16 final size:16
Alignment explanation
Indices: 40514--40548 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40504 TTTCATGTAT
40514 TTATTATATTACATTA
1 TTATTATATTACATTA
* *
40530 TTATTATTTTACTTTA
1 TTATTATATTACATTA
40546 TTA
1 TTA
40549 AATTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTATATTACATTA
Found at i:40555 original size:21 final size:22
Alignment explanation
Indices: 40529--40578 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
40519 ATATTACATT
*
40529 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
*
40550 ATTATT-TTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
40571 TTTATTAT
1 ATTATTAT
40579 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:45504 original size:36 final size:36
Alignment explanation
Indices: 45457--45560 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
45447 GTGCTCACCA
45457 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
**
45493 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* * *
45529 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
45561 TAAACATTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:45651 original size:37 final size:37
Alignment explanation
Indices: 45592--45662 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
45582 TTGAAATGAG
* *
45592 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
45629 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
45663 TAAACATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:45679 original size:102 final size:102
Alignment explanation
Indices: 45475--45865 Score: 651
Period size: 102 Copynumber: 3.9 Consensus size: 102
45465 CTTGAGACAG
** * * * *
45475 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AATTTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
45539 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
45576 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
45641 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
45678 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
45743 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * * *
45780 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAA-TAAATTTTGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
45844 TGAGACAGTTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
45866 CAAAACCTTT
Statistics
Matches: 275, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
101 80 0.29
102 195 0.71
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:45745 original size:37 final size:37
Alignment explanation
Indices: 45678--45764 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
45668 ATTGGAAACA
** * *
45678 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
45714 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
45751 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
45765 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:45824 original size:204 final size:202
Alignment explanation
Indices: 45475--45932 Score: 673
Period size: 204 Copynumber: 2.2 Consensus size: 202
45465 CTTGAGACAG
* *
45475 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAATTTTTTTCTCCCTT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTT
* *
45540 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCTT
66 GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCTT
* * *
45605 GAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
131 GAGATAATTTCCCTTGAAA-AAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACAT
45670 TGGAAACA
195 TGGAAACA
** * *
45678 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCT
45743 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCT
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCT
* * *
45808 TGAGATAATTTCCCTTGAAATAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACACAAAACC
130 TGAGATAATTTCCCTTGAAAAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACA-TAAACA
* ***
45873 TTTGAGATTG
194 TTGGA-AACA
* * * * *
45883 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
45933 CAAAATCTTT
Statistics
Matches: 227, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
203 80 0.35
204 104 0.46
205 43 0.19
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (202 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCGTCTCTCTT
GAGATAATTTCCCTTGAAAAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATT
GGAAACA
Found at i:45826 original size:36 final size:36
Alignment explanation
Indices: 45779--45863 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
45769 CATTGAAAAC
* *
45779 ATTTCCCTTGAAATGAATTTCGTCTCTC-TTGAGATA
1 ATTTCCCTTGAAATAAATTTCGTCTC-CATTGAGACA
*
45815 ATTTCCCTTGAAATAAATTTTGTCTCCATTGAGACA
1 ATTTCCCTTGAAATAAATTTCGTCTCCATTGAGACA
* *
45851 GTTTCTCTTGAAA
1 ATTTCCCTTGAAA
45864 CACAAAACCT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.02
36 42 0.98
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
ATTTCCCTTGAAATAAATTTCGTCTCCATTGAGACA
Found at i:45956 original size:67 final size:67
Alignment explanation
Indices: 45807--45965 Score: 216
Period size: 67 Copynumber: 2.4 Consensus size: 67
45797 TTCGTCTCTC
** *
45807 TTGAGATAATTTCCCTTGAAATAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACACAAAAC
45872 CT
66 CT
*
45874 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCA-TGAGACAGTTTCTCTTGAAACACAAAA
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-CCATTGAGACAGTTTCTCTTGAAACACAAAA
*
45938 TCT
65 CCT
*
45941 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
45966 ATTTCATTTC
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 74 0.90
68 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:46775 original size:108 final size:109
Alignment explanation
Indices: 46545--47014 Score: 598
Period size: 109 Copynumber: 4.4 Consensus size: 109
46535 TAGCTAGAGT
* * * *
46545 CAAGTTC-ACTTCACAACGAAGGGACGTCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
46608 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* *
46652 CAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
46717 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGA-AACA
66 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * ** * **
46760 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAAC-C
* *
46824 GATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACA
65 GATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
* * * ** * * * *
46869 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
* * *
46934 ATTTCAACTTCGCA-G-CGAAGGATAT--TG-GACTCGAGACAACA
66 ATTTCAAC-TC-CACGACGGAGGATATCGTGCTACCCGAGACAACA
*
46975 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
47015 AAGATTTCGT
Statistics
Matches: 321, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
106 50 0.16
107 10 0.03
108 124 0.39
109 131 0.41
110 4 0.01
111 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (109 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCG
ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACA
Found at i:46940 original size:217 final size:215
Alignment explanation
Indices: 46606--47169 Score: 600
Period size: 217 Copynumber: 2.7 Consensus size: 215
46596 ATTTCGGAAC
*
46606 CGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 CGATTTCAACTCCACGACGGAGGATATCGTGCCACCCGAGACAACACAAGTTCAACTTCACAACG
** * * *
46671 AAGGGATGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCGATTTCAAC-TC-CACGACG
66 AAGGGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTTCGCA-G-CG
* * *
46734 GAGGATATCGTGCTACCCGAGA-AACACAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCA
129 AAGGATAT--TG-GACCCGAGACAACACAAGTCCAACTTCACAACGAAGGGACGGCTGATTGTCA
46798 ATGAACAACTTTTCAGTTTCATCCG
191 ATGAACAACTTTTCAGTTTCATCCG
* *
46823 CGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAATG
1 CGATTTCAACTCCACGACGGAGGATATCGTGCCACCCGAGACAACACAAGTTCAACTTCACAACG
** * * *
46888 AAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTCGCAGCGAA
66 AAGGGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTTCGCAGCGAA
* *
46953 GGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTC----AA
131 GGATATTGGACCCGAGACAACACAAGTCCAACTTCACAACGAAGGGACGGCTGATTGTCAATGAA
** **
47014 CAAGATTTC-G-TTCA-GAG
196 CAACTTTTCAGTTTCATCCG
* * * * * * *
47031 TCAATTTCATCTTCAC-AGCGAAGGATAT--TAG--ACTCGAGACAGCACAAGCTCAACTTCACA
1 -CGATTTCAACTCCACGA-CGGAGGATATCGT-GCCACCCGAGACAACACAAGTTCAACTTCACA
* * * ** * * * *
47091 GCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCAATTTCAACTTCACAGC
63 ACGAAGGGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTTCGCAGC
*
47156 GGAGGATATTGGAC
128 GAAGGATATTGGAC
47170 TCGGAACAAT
Statistics
Matches: 299, Mismatches: 42, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
206 92 0.31
207 1 0.00
208 3 0.01
209 25 0.08
210 1 0.00
211 9 0.03
214 7 0.02
215 41 0.14
217 115 0.38
218 3 0.01
219 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (215 bp):
CGATTTCAACTCCACGACGGAGGATATCGTGCCACCCGAGACAACACAAGTTCAACTTCACAACG
AAGGGACAGCTGGTTGTCAACAAACAACTTCCAAATTCCAGAACCAATTTCAACTTCGCAGCGAA
GGATATTGGACCCGAGACAACACAAGTCCAACTTCACAACGAAGGGACGGCTGATTGTCAATGAA
CAACTTTTCAGTTTCATCCG
Found at i:47084 original size:100 final size:102
Alignment explanation
Indices: 46545--47172 Score: 462
Period size: 108 Copynumber: 5.9 Consensus size: 102
46535 TAGCTAGAGT
* * * * * * * *
46545 CAAGTTC-ACTTCACAACGAAGGGACGTCTGGTTGCCAACAACAATTTCCCAATTTCGGAACCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTT--C-AGTTCAGAGCCAA
* * * *
46609 TTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACA
63 TTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACA
* * * * * * *
46652 CAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCG
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-AAATT-TCAGTT-CAGAGCCA
* * * *
46717 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGA-AACA
62 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACA
* * * * **
46760 CAAGTCCAACTTCACAACGAAGGGACGGCTGGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGC
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAA-CAA-AA-ATTTCAG-TTCAGAGC-C
* * * *
46824 GATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACA
61 AATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACA
* * * * *
46869 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-A-ATTTC--AGTTCAGAGCCA
*
46934 ATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACA
62 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* *
46975 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGATTTC-GTTCAGAGTCAATTT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGAGCCAATTT
* * *
47038 CATCTTCACAGCGAAGGATATTAGACTCGAGACAGCA
66 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* * * * *
47075 CAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-AATTT--CAGTT-CAGAGCCA
*
47140 ATTTCAACTTCACAGCGGAGGATATTGGACTCG
62 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
47173 GAACAATATT
Statistics
Matches: 448, Mismatches: 52, Indels: 43
0.83 0.10 0.08
Matches are distributed among these distances:
100 82 0.18
101 2 0.00
102 4 0.01
103 4 0.01
104 1 0.00
105 5 0.01
106 86 0.19
107 11 0.02
108 129 0.29
109 118 0.26
110 6 0.01
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (102 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
Found at i:47697 original size:35 final size:37
Alignment explanation
Indices: 47630--47701 Score: 112
Period size: 35 Copynumber: 2.0 Consensus size: 37
47620 CTTTTTCGTC
47630 CTACTAGGATTCAAACTCTCAAAAATAAGATAGAATT
1 CTACTAGGATTCAAACTCTCAAAAATAAGATAGAATT
* *
47667 CTACTAGGATTC-AACTCT-TAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCTCAAAAATAAGATAGAATT
47702 TTGCTATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 15 0.45
36 6 0.18
37 12 0.36
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCTCAAAAATAAGATAGAATT
Found at i:48194 original size:11 final size:11
Alignment explanation
Indices: 48174--48256 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
48164 TTAATTATTT
*
48174 TTATTCTAATA
1 TTATTTTAATA
*
48185 TTATTTTAATG
1 TTATTTTAATA
48196 TT-TTTTAA-A
1 TTATTTTAATA
*
48205 GTTATTATATATA
1 -TTATTTTA-ATA
*
48218 TATATTATAACTA
1 T-TATTTTAA-TA
*
48231 TTATATTTATTA
1 TTAT-TTTAATA
*
48243 TTATTTTACTA
1 TTATTTTAATA
48254 TTA
1 TTA
48257 ACGTATAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 12 0.21
13 14 0.24
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:48444 original size:16 final size:16
Alignment explanation
Indices: 48423--48456 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48413 CATGTATTTA
48423 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
48439 TATTATTTTACTTTAT
1 TATTATATTACATTAT
48455 TA
1 TA
48457 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:52060 original size:35 final size:35
Alignment explanation
Indices: 52021--52262 Score: 83
Period size: 35 Copynumber: 6.9 Consensus size: 35
52011 AAGTCATGTC
52021 GAAAACTGTCTCAAGTGAGACAAAATTTTTCAAAA
1 GAAAACTGTCTCAAGTGAGACAAAATTTTTCAAAA
* * * ** *
52056 GAAAA-TATATCGAA-T--G-CGATTTTGTTTCGAGAA
1 GAAAACTGTCTC-AAGTGAGACAAAATT-TTTC-AAAA
* *
52089 -AAAA-TATCTCAAGTGAGATAAAAATAAATTGTTTCAAAA
1 GAAAACTGTCTCAAGTGAGA-CAAAAT---TT-TT-CAAAA
* *
52128 G-AAACTGTCTCGAGTGCGACGAAAA-TTTT-AAAGA
1 GAAAACTGTCTCAAGTGAGAC-AAAATTTTTCAAA-A
* * * *** *
52162 GAAAACTATCTCAAGCGAGATAAAAAAATTCAAGA
1 GAAAACTGTCTCAAGTGAGACAAAATTTTTCAAAA
* ** * *
52197 G-AAACTGTCTCGAGTGAGATGAAACTTTTCAAAT
1 GAAAACTGTCTCAAGTGAGACAAAATTTTTCAAAA
* **
52231 GAAAACTGTCTCGAGTGAGATGAAATTTTTCA
1 GAAAACTGTCTCAAGTGAGACAAAATTTTTCA
52263 TGCGAAACAA
Statistics
Matches: 152, Mismatches: 34, Indels: 42
0.67 0.15 0.18
Matches are distributed among these distances:
31 6 0.04
32 15 0.10
33 6 0.04
34 37 0.24
35 56 0.37
36 6 0.04
38 1 0.01
39 9 0.06
40 16 0.11
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (35 bp):
GAAAACTGTCTCAAGTGAGACAAAATTTTTCAAAA
Found at i:52165 original size:34 final size:34
Alignment explanation
Indices: 52127--52260 Score: 135
Period size: 35 Copynumber: 3.9 Consensus size: 34
52117 TTGTTTCAAA
* *
52127 AGAAACTGTCTCGAGTGCGACGAAAATTTTAAAG
1 AGAAACTGTCTCGAGTGAGATGAAAATTTTAAAG
* * * * ** *
52161 AGAAAACTATCTCAAGCGAGATAAAAAAATTCAAG
1 AG-AAACTGTCTCGAGTGAGATGAAAATTTTAAAG
*
52196 AGAAACTGTCTCGAGTGAGATGAAACTTTTCAAATG
1 AGAAACTGTCTCGAGTGAGATGAAAATTTT-AAA-G
*
52232 A-AAACTGTCTCGAGTGAGATGAAATTTTT
1 AGAAACTGTCTCGAGTGAGATGAAAATTTT
52261 CATGCGAAAC
Statistics
Matches: 79, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
34 23 0.29
35 54 0.68
36 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.25
Consensus pattern (34 bp):
AGAAACTGTCTCGAGTGAGATGAAAATTTTAAAG
Found at i:52270 original size:69 final size:69
Alignment explanation
Indices: 52121--52251 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 69
52111 AATAAATTGT
* *
52121 TTCAAAAGAAACTGTCTCGAGTGCGACGAAAATTTTAAAGAGAAAACTATCTCAAGCGAGATAAA
1 TTCAAGAGAAACTGTCTCGAGTGAGACGAAAATTTTAAAGAGAAAACTATCTCAAGCGAGATAAA
52186 AAAA
66 AAAA
* * * * * *
52190 TTCAAGAGAAACTGTCTCGAGTGAGATGAAACTTTTCAAA-TGAAAACTGTCTCGAGTGAGAT
1 TTCAAGAGAAACTGTCTCGAGTGAGACGAAAATTTT-AAAGAGAAAACTATCTCAAGCGAGAT
52252 GAAATTTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
69 50 0.94
70 3 0.06
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (69 bp):
TTCAAGAGAAACTGTCTCGAGTGAGACGAAAATTTTAAAGAGAAAACTATCTCAAGCGAGATAAA
AAAA
Found at i:58348 original size:20 final size:20
Alignment explanation
Indices: 58323--58360 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58313 TTCCCTTTCA
*
58323 AAGGGGGAATCGGTTCCCCC
1 AAGGGGGAATCGATTCCCCC
*
58343 AAGGGGGGATCGATTCCC
1 AAGGGGGAATCGATTCCC
58361 TCTGCACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (20 bp):
AAGGGGGAATCGATTCCCCC
Found at i:66174 original size:15 final size:16
Alignment explanation
Indices: 66147--66188 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
66137 CTATTTGTCT
66147 ATCTTTTTCTCCTTCTC
1 ATCTTTTTCTCC-TCTC
66164 -TCTTTTT-TCCTCTC
1 ATCTTTTTCTCCTCTC
*
66178 ATCTTTCTCTC
1 ATCTTTTTCTC
66189 TCTTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 9 0.41
ACGTcount: A:0.05, C:0.36, G:0.00, T:0.60
Consensus pattern (16 bp):
ATCTTTTTCTCCTCTC
Found at i:70144 original size:37 final size:35
Alignment explanation
Indices: 70098--70184 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 35
70088 TGGCAATCAA
70098 TTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 TTTTG-AAAAATGATTTTCAAAGTTTGGTAAATG-TT
* *
70135 TTTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTT
1 TTTTGAAAAATGA-TTTTCAAAGTTTGGTAAATGTT
*
70171 TGTTGAAAAATGAT
1 TTTTGAAAAATGAT
70185 AATGGGATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 1 0.02
36 20 0.44
37 24 0.53
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (35 bp):
TTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTT
Found at i:74681 original size:35 final size:35
Alignment explanation
Indices: 74641--74719 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
74631 CCAACTTTGA
* *
74641 AAAAATGATTTTCAAAATTTGGTAAATGTTTTTTTG
1 AAAAATGATTTTCAAAATTTAGTAAATG-TTTGTTG
* *
74677 -AAAATGGTTTTCAAAGTTTAGTAAATGTTTGTTG
1 AAAAATGATTTTCAAAATTTAGTAAATGTTTGTTG
74711 AAAAATGAT
1 AAAAATGAT
74720 AATAGGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 6 0.16
35 31 0.84
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (35 bp):
AAAAATGATTTTCAAAATTTAGTAAATGTTTGTTG
Found at i:75825 original size:2 final size:2
Alignment explanation
Indices: 75818--75850 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
75808 ACTGGGAACC
75818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
75851 TTTTCTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78216 original size:2 final size:2
Alignment explanation
Indices: 78211--78251 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
78201 TCGGATTCGA
78211 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78252 GAATATGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79712 original size:2 final size:2
Alignment explanation
Indices: 79701--79742 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
79691 GAAAAACCAT
79701 TA TA TA -A 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
79742 T
1 T
79743 CAAGCTCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83056 original size:19 final size:19
Alignment explanation
Indices: 83029--83068 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
83019 CCTGTTACAA
83029 CCCGACCCGACCCGTTCAC
1 CCCGACCCGACCCGTTCAC
* *
83048 CCCGCCCCGACCCGTTGAC
1 CCCGACCCGACCCGTTCAC
83067 CC
1 CC
83069 GTTGACCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.60, G:0.17, T:0.10
Consensus pattern (19 bp):
CCCGACCCGACCCGTTCAC
Found at i:83775 original size:36 final size:36
Alignment explanation
Indices: 83728--83800 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
83718 AGTTCTGAAA
83728 TTAAGTGATAAAAGAATCAGCCATCGATATATAGAT
1 TTAAGTGATAAAAGAATCAGCCATCGATATATAGAT
* * *
83764 TTAAGTGATAAAAGAATCAGTCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAGCCATCGATATATAGAT
83800 T
1 T
83801 ATAATTTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.30
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAGCCATCGATATATAGAT
Found at i:85390 original size:24 final size:24
Alignment explanation
Indices: 85363--85450 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
85353 ATTTCCGACT
*
85363 TGAATTCTGTTCTGATACATGACC
1 TGAATTCTGTTCTGATACATGATC
*
85387 TGAATTCTGTTCTGATTTC-TGATC
1 TGAATTCTGTTCTGA-TACATGATC
* * * *
85411 TGGATTCTGTTATGATATATGTTC
1 TGAATTCTGTTCTGATACATGATC
*
85435 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
85451 TTCTGATATC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATACATGATC
Found at i:85401 original size:12 final size:12
Alignment explanation
Indices: 85363--85455 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
85353 ATTTCCGACT
85363 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
85375 TG-ATACATGACC
1 TGAATTC-TGTTC
85387 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
85399 TGATTTCTGATC
1 TGAATTCTGTTC
* *
85411 TGGATTCTGTTA
1 TGAATTCTGTTC
*
85423 TG-ATATATGTTC
1 TGAAT-TCTGTTC
*
85435 TGAATTCTGTTT
1 TGAATTCTGTTC
*
85447 TGATTTCTG
1 TGAATTCTG
85456 ATATCTCCGT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 5 0.08
12 50 0.83
13 5 0.08
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:85454 original size:48 final size:48
Alignment explanation
Indices: 85349--85457 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
85339 AAATATTTTA
* * *
85349 TCTGATTTCCGA-CTTGAATTCTGTTCTGATACATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTATGATACATGACCTGAATTCTGT
* **
85397 TCTGATTTCTGATCTGGATTCTGTTATGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTATGATACATGACCTGAATTCTGT
*
85445 TTTGATTTCTGAT
1 TCTGATTTCTGAT
85458 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTATGATACATGACCTGAATTCTGT
Found at i:87074 original size:31 final size:31
Alignment explanation
Indices: 86995--87081 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
86985 TGCCAATGCC
* * *
86995 TATATACATATGATACTATCATCTCAATGTT
1 TATATACATATGATATTATCATGTCAATGTA
* *
87026 TATGTACACATGATATTATCATGTCAATGTA
1 TATATACATATGATATTATCATGTCAATGTA
* * *
87057 TATATACATGTGGTATTATTATGTC
1 TATATACATATGATATTATCATGTC
87082 GTTTTAAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (31 bp):
TATATACATATGATATTATCATGTCAATGTA
Found at i:88843 original size:26 final size:28
Alignment explanation
Indices: 88791--88843 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 28
88781 ATAAGGGTTT
*
88791 TTTTTCTTTCTAATAATTTTAGGATTTA
1 TTTTTCTTTCTAATAATTTGAGGATTTA
* *
88819 TTTTTC-TT-TAATTATTTGAGTATTT
1 TTTTTCTTTCTAATAATTTGAGGATTT
88844 TTATTTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 14 0.64
27 2 0.09
28 6 0.27
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.64
Consensus pattern (28 bp):
TTTTTCTTTCTAATAATTTGAGGATTTA
Found at i:88950 original size:14 final size:14
Alignment explanation
Indices: 88933--88962 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88923 AAATTAATAG
88933 ACATAAACGAACGA
1 ACATAAACGAACGA
*
88947 ACATAAATGAACGA
1 ACATAAACGAACGA
88961 AC
1 AC
88963 GATCCCTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (14 bp):
ACATAAACGAACGA
Found at i:90100 original size:71 final size:71
Alignment explanation
Indices: 89984--90129 Score: 258
Period size: 71 Copynumber: 2.1 Consensus size: 71
89974 CATCAATATC
* *
89984 CATTTAATCATTGACTTGATACTCTCCTGAATGTGGTAGCACTATCTGACATTCACCATTTTGAA
1 CATTTAATCATTGACCTGATACTCTCCTGAATATGGTAGCACTATCTGACATTCACCATTTTGAA
90049 TCACCT
66 TCACCT
*
90055 CATTTAATCATTGACCTGATACTCTCCTGAATATGGTAGCACTATCTGGCATTCACCATTTTGAA
1 CATTTAATCATTGACCTGATACTCTCCTGAATATGGTAGCACTATCTGACATTCACCATTTTGAA
90120 TCACCT
66 TCACCT
90126 -ATTT
1 CATTT
90130 TCTATTCATA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 4 0.06
71 68 0.94
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (71 bp):
CATTTAATCATTGACCTGATACTCTCCTGAATATGGTAGCACTATCTGACATTCACCATTTTGAA
TCACCT
Found at i:90654 original size:31 final size:31
Alignment explanation
Indices: 90616--90725 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
90606 GTCAAGGTCG
*
90616 AGTGATTGATTTGTTATAAATTAATAATGTT
1 AGTGATTGATTTGTTATAAATTGATAATGTT
*
90647 AGTGATTGATTTGTTACAAATTGATAATGTT
1 AGTGATTGATTTGTTATAAATTGATAATGTT
* *
90678 AGTGATTGATTTATTATAAATTGATAATATT
1 AGTGATTGATTTGTTATAAATTGATAATGTT
* * *
90709 AATGACTAATTTGTTAT
1 AGTGATTGATTTGTTAT
90726 TTTTGAAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.47
Consensus pattern (31 bp):
AGTGATTGATTTGTTATAAATTGATAATGTT
Found at i:90685 original size:16 final size:16
Alignment explanation
Indices: 90639--90687 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
90629 TTATAAATTA
90639 ATAATGTTAGTGATTG
1 ATAATGTTAGTGATTG
* ***
90655 AT-TTGTTACAAATTG
1 ATAATGTTAGTGATTG
90670 ATAATGTTAGTGATTG
1 ATAATGTTAGTGATTG
90686 AT
1 AT
90688 TTATTATAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (16 bp):
ATAATGTTAGTGATTG
Found at i:109400 original size:23 final size:23
Alignment explanation
Indices: 109342--109402 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
109332 CTCGTATAAA
* *
109342 TGCACCTAAGTGACACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
109365 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
109388 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
109403 TATAAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:114460 original size:3 final size:3
Alignment explanation
Indices: 114452--114478 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
114442 TCATTATCAA
114452 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
114479 CATTTATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:114733 original size:23 final size:23
Alignment explanation
Indices: 114715--114775 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
114705 CTCGTATAAA
*
114715 TACACCTAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
114738 TAAACCGAAGTGCCACGTAGAAT
1 TACACCGAAGTGCCACGTAGAAT
*
114761 TGCACCGAAGTGCCA
1 TACACCGAAGTGCCA
114776 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (23 bp):
TACACCGAAGTGCCACGTAGAAT
Found at i:119004 original size:15 final size:15
Alignment explanation
Indices: 118986--119052 Score: 98
Period size: 15 Copynumber: 4.5 Consensus size: 15
118976 TAGCCACCTA
118986 GTGGATAACCTTGAG
1 GTGGATAACCTTGAG
119001 GTGGATAACCTTGAG
1 GTGGATAACCTTGAG
*
119016 GTGGATAACTTTGAG
1 GTGGATAACCTTGAG
* *
119031 GCGGATACCCTTGAG
1 GTGGATAACCTTGAG
*
119046 GGGGATA
1 GTGGATA
119053 TCCTCCATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.25
Consensus pattern (15 bp):
GTGGATAACCTTGAG
Found at i:122221 original size:24 final size:24
Alignment explanation
Indices: 122189--122238 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
122179 CCGTAGATGT
122189 TGCTGTAAATATTTATCATAACAC
1 TGCTGTAAATATTTATCATAACAC
122213 TGCTGTAAATATTTATCATAACAC
1 TGCTGTAAATATTTATCATAACAC
122237 TG
1 TG
122239 GACAGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (24 bp):
TGCTGTAAATATTTATCATAACAC
Found at i:129824 original size:16 final size:17
Alignment explanation
Indices: 129803--129848 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
129793 CCCATTTCTT
129803 AATATTAAAA-AATATA
1 AATATTAAAACAATATA
*
129819 AATATTAAAATAAT-TA
1 AATATTAAAACAATATA
129835 AA-A-TAAAACAATAT
1 AATATTAAAACAATAT
129849 GTATTTTCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 14 0.52
17 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATTAAAACAATATA
Found at i:130008 original size:11 final size:11
Alignment explanation
Indices: 129992--130053 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
129982 AGATTAAGAT
129992 AAATAATAATA
1 AAATAATAATA
130003 AAATAATAATTA
1 AAATAATAA-TA
*
130015 AAGCT-ATAATTA
1 AA-ATAATAA-TA
130027 AAAT-AT-A-A
1 AAATAATAATA
*
130035 AAGTAATAATA
1 AAATAATAATA
130046 AAATAATA
1 AAATAATA
130054 TTGCAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 20 0.48
12 13 0.31
13 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (11 bp):
AAATAATAATA
Found at i:130062 original size:17 final size:18
Alignment explanation
Indices: 130042--130082 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
130032 TAAAAGTAAT
*
130042 AATAAAATAAT-ATTGCA
1 AATAAAATAATGATTGAA
*
130059 AAT-AAATAATGATTTAA
1 AATAAAATAATGATTGAA
130076 AATAAAA
1 AATAAAA
130083 GAAATTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 10 0.50
18 3 0.15
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AATAAAATAATGATTGAA
Done.