Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006333.1 Hibiscus syriacus cultivar Beakdansim tig00015138_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: 105520
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:101 original size:21 final size:20
Alignment explanation
Indices: 60--107 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
50 CTACAAACAT
* *
60 ATTTTTTCATAATAAACTAAA
1 ATTTTTTCATAAAAAAAT-AA
81 ATTTTTT-ATTAAAAAAATAA
1 ATTTTTTCA-TAAAAAAATAA
101 ATTTTTT
1 ATTTTTT
108 GTTATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTTCATAAAAAAATAA
Found at i:922 original size:403 final size:401
Alignment explanation
Indices: 168--951 Score: 963
Period size: 404 Copynumber: 1.9 Consensus size: 401
158 TTTTGGAACC
* *
168 AAAAAATACGGAAAAAATGTTTATGATATATAATTTTACATAATGAAAAATATATAACTAAAAAA
1 AAAAAATACGGAAAAAATGGTTATGA-ATATAATTTTACAGAATGAAAAATATATAACTAAAAAA
** *
233 TAATTGATTACAAAAAATTTTAAATTTTATTGTCTGATATGATAATTTTTTATAACAAACTATAA
65 TAATTGATTACAAAAAATCCTAAATTTTATTATCTGATATGATAATTTTTTATAACAAACTATAA
* * *
298 ATTATAATTACAAAACTTATGAATAACTATTTGAAACAAAAAAAAATGGAGAAAAAATATTATCA
130 ATTATAATTACAAAAATTATCAATAACTATTTGAAACAAAAAAAAATGGAGAAAAAATATAATCA
* * *
363 CAATATTTTTCACTATAATTAAAATTTATAAGTACAAGTATAATTTGTCACAAAAATGTGAATAC
195 CAATATTTATCACTATAATTAAAATTTATAACTACAAATATAATTTGTCACAAAAATGTGAATAC
* *
428 CATTATTTTTTGTGACAATATTTTTTATAATAATTATACACACTTATAGTTACAAAAATTGTTAC
260 CATTATTTTTTGTGACAATATTTTCTATAATAATTATACACACTTATAGTTACAAAAATTGTCAC
* *
493 TATATGATTTTTTTTGGAGCAAAAAATATGGAG-GAAAATCTTTATGACAATAT-TTTGTTATTA
325 TATATGACTTTTTTTGG-G-AAAAAAAATGGAGTG-AAAT-TTTATGACAATATATTTGTTATTA
556 TAATATTTTTACAGTA
386 TAATATTTTTACAGTA
* * *
572 AAAAAATA-GGGATAAATGGTTATG-ATATAATTTT-CAGAATGATTAAAATATATAAGTAAAAA
1 AAAAAATACGGAAAAAATGGTTATGAATATAATTTTACAGAATGA--AAAATATATAACT-AAAA
* * * *
634 AATAATTGATTACAAAAAA-CCTGAATTTTATTATTTGATGTTATAATTTTTTTCTATAACAATA
63 AATAATTGATTACAAAAAATCCTAAATTTTATTATCTGATATGATAA--TTTTT-TATAAC-A-A
* *
698 ACTATAAATTATAATTATAAAAATTGTCAAT-ACT-TTTGAAAC-AAAAAAAA-GGA-AAAATAA
123 ACTATAAATTATAATTACAAAAATTATCAATAACTATTTGAAACAAAAAAAAATGGAGAAAA-AA
* * * *
758 T-TAATGACAATATATATATCACTATAGTTAAAATTTATAACTACAAA-ATATATTTGTTATAAA
187 TATAATCACAATAT-T-TATCACTATAATTAAAATTTATAACTACAAATATA-ATTTGTCACAAA
* *
821 AATTTGAATATCC-TTATTTTTTGTGACAATGTTTTCTATAATAA-TATTA-ACACTTATAGTTA
249 AATGTGAATA-CCATTATTTTTTGTGACAATATTTTCTATAATAATTA-TACACACTTATAGTTA
* * * *
883 CAAAATTTGTCATTATA-GACTTTTTTTGCGCAAAAAAAATGGAGTGAAATTTTGTGACAATATA
312 CAAAAATTGTCACTATATGACTTTTTTTG-GGAAAAAAAATGGAGTGAAATTTTATGACAATATA
947 TTTGT
376 TTTGT
952 CACTATTAAA
Statistics
Matches: 329, Mismatches: 34, Indels: 37
0.82 0.09 0.09
Matches are distributed among these distances:
400 19 0.06
401 31 0.09
402 57 0.17
403 76 0.23
404 98 0.30
405 16 0.05
406 4 0.01
407 28 0.09
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (401 bp):
AAAAAATACGGAAAAAATGGTTATGAATATAATTTTACAGAATGAAAAATATATAACTAAAAAAT
AATTGATTACAAAAAATCCTAAATTTTATTATCTGATATGATAATTTTTTATAACAAACTATAAA
TTATAATTACAAAAATTATCAATAACTATTTGAAACAAAAAAAAATGGAGAAAAAATATAATCAC
AATATTTATCACTATAATTAAAATTTATAACTACAAATATAATTTGTCACAAAAATGTGAATACC
ATTATTTTTTGTGACAATATTTTCTATAATAATTATACACACTTATAGTTACAAAAATTGTCACT
ATATGACTTTTTTTGGGAAAAAAAATGGAGTGAAATTTTATGACAATATATTTGTTATTATAATA
TTTTTACAGTA
Found at i:1463 original size:15 final size:15
Alignment explanation
Indices: 1443--1477 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1433 CAAAAAAAAT
1443 ATTAATAGTGACAAA
1 ATTAATAGTGACAAA
**
1458 ATTAATTTTGACAAA
1 ATTAATAGTGACAAA
1473 ATTAA
1 ATTAA
1478 ATTTGTCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (15 bp):
ATTAATAGTGACAAA
Found at i:1491 original size:15 final size:15
Alignment explanation
Indices: 1451--1482 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1441 ATATTAATAG
*
1451 TGACAAAATTAATTT
1 TGACAAAATTAAATT
1466 TGACAAAATTAAATT
1 TGACAAAATTAAATT
1481 TG
1 TG
1483 TCACAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:11821 original size:16 final size:16
Alignment explanation
Indices: 11783--11827 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
11773 AAACAGACTT
11783 GTTTGTTTTCTACA-A
1 GTTTGTTTTCTACACA
*
11798 -TCTGTTTTCTACACA
1 GTTTGTTTTCTACACA
11813 GTTTGTTTTCTACAC
1 GTTTGTTTTCTACAC
11828 TAAGTCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 13 0.50
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (16 bp):
GTTTGTTTTCTACACA
Found at i:15033 original size:16 final size:17
Alignment explanation
Indices: 15012--15044 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15002 AAGAAGTTGT
*
15012 CACCAAC-CTTCAATTC
1 CACCAACGCATCAATTC
15028 CACCAACGCATCAATTC
1 CACCAACGCATCAATTC
15045 TCGAATCAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.42, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCAACGCATCAATTC
Found at i:19645 original size:198 final size:198
Alignment explanation
Indices: 19307--19716 Score: 802
Period size: 198 Copynumber: 2.1 Consensus size: 198
19297 GCATCATCGG
19307 CTAATAAATCAACAAAATTAACTGACCCTTATTCCCATATGTGATGAGGTAAGGGGGAGGTAGGA
1 CTAATAAATCAACAAAATTAACTGACCCTTATTCCCATATGTGATGAGGTAAGGGGGAGGTAGGA
*
19372 TAGTAGGCTGCCCCTAACGCCAAGTTGAGAGCAGCTTCCGTATGAGACCTCCAAATTATGAAATG
66 TAGTAGGCTGCCCCTAACGCCAAGTTGAGAGCAGCTTCCGTAAGAGACCTCCAAATTATGAAATG
19437 TCTTCCGTGAGACTCGAATCCCACGACCCCAAAATTAATAACCAACTGAGCTGGATGGTCATTTC
131 TCTTCCGTGAGACTCGAATCCCACGACCCCAAAATTAATAACCAACTGAGCTGGATGGTCATTTC
19502 CGA
196 CGA
*
19505 CTAATAAATCAACAAAATTAACTGACCCTTATTCCCATATGTGATGGGGTAAGGGGGAGGTAGGA
1 CTAATAAATCAACAAAATTAACTGACCCTTATTCCCATATGTGATGAGGTAAGGGGGAGGTAGGA
19570 TAGTAGGCTGCCCCTAACGCCAAGTTGAGAGCAGCTTCCGTAAGAGACCTCCAAATTATGAAATG
66 TAGTAGGCTGCCCCTAACGCCAAGTTGAGAGCAGCTTCCGTAAGAGACCTCCAAATTATGAAATG
19635 TCTTCCGTGAGACTCGAATCCCACGACCCCAAAATTAATAACCAACTGAGCTGGATGGTCATTTC
131 TCTTCCGTGAGACTCGAATCCCACGACCCCAAAATTAATAACCAACTGAGCTGGATGGTCATTTC
19700 CGA
196 CGA
19703 CTAATAAATCAACA
1 CTAATAAATCAACA
19717 GAAGACCCCA
Statistics
Matches: 210, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
198 210 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (198 bp):
CTAATAAATCAACAAAATTAACTGACCCTTATTCCCATATGTGATGAGGTAAGGGGGAGGTAGGA
TAGTAGGCTGCCCCTAACGCCAAGTTGAGAGCAGCTTCCGTAAGAGACCTCCAAATTATGAAATG
TCTTCCGTGAGACTCGAATCCCACGACCCCAAAATTAATAACCAACTGAGCTGGATGGTCATTTC
CGA
Found at i:20655 original size:33 final size:33
Alignment explanation
Indices: 20618--20714 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
20608 TATGAAATGA
* *
20618 CATATTATGATCAATATAGTAAGGATTATGCTG
1 CATATTATGATCAATATATTAAGGAATATGCTG
* *
20651 CATATTATGCTCAATATATTAAGGAATACGCTG
1 CATATTATGATCAATATATTAAGGAATATGCTG
*
20684 CATATCATGATCAATATATTAAGGAATATGC
1 CATATTATGATCAATATATTAAGGAATATGC
20715 CGCAGCTGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
CATATTATGATCAATATATTAAGGAATATGCTG
Found at i:23140 original size:3 final size:3
Alignment explanation
Indices: 23132--23156 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
23122 CCGTTATCCG
23132 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
23157 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:26731 original size:25 final size:25
Alignment explanation
Indices: 26701--26748 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
26691 TAAAATTTAA
26701 ATAATTTA-TTTTAAAACAAAAAATT
1 ATAATTTAGTTTTAAAA-AAAAAATT
*
26726 ATAATTTAGTTTTTAAAAAAAAA
1 ATAATTTAGTTTTAAAAAAAAAA
26749 CAAATTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAATTTAGTTTTAAAAAAAAAATT
Found at i:28647 original size:20 final size:19
Alignment explanation
Indices: 28602--28652 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
28592 TATTAAATAA
28602 ATGGTTTGATAAATTTAAT
1 ATGGTTTGATAAATTTAAT
*
28621 ATGGGTTTTATAAATTTAGACT
1 AT-GGTTTGATAAATTTA-A-T
28643 -TGGTTTGATA
1 ATGGTTTGATA
28653 GGTTTGCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 2 0.07
22 1 0.04
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (19 bp):
ATGGTTTGATAAATTTAAT
Found at i:36024 original size:44 final size:45
Alignment explanation
Indices: 35965--36055 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 45
35955 AATCGTTTTA
*
35965 AAAACTTATAATTAAAATTAATGCAAAACTTAATATTTAACAACT
1 AAAACTTATAATTAAAATTAATGCAAAACTTAAAATTTAACAACT
* * * *
36010 AAAA-TTATAATTAAAGTTAATGCAGAATTTAAAATTTAATAACT
1 AAAACTTATAATTAAAATTAATGCAAAACTTAAAATTTAACAACT
36054 AA
1 AA
36056 CTATATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.34
Consensus pattern (45 bp):
AAAACTTATAATTAAAATTAATGCAAAACTTAAAATTTAACAACT
Found at i:36063 original size:44 final size:44
Alignment explanation
Indices: 35967--36065 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
35957 TCGTTTTAAA
*
35967 AACT-TATAATTAAAATTAATGCAAAACTTAATATTTAACAACT
1 AACTATATAATTAAAATTAATGCAAAACTTAAAATTTAACAACT
* * * * *
36010 AA-AATTATAATTAAAGTTAATGCAGAATTTAAAATTTAATAACT
1 AACTA-TATAATTAAAATTAATGCAAAACTTAAAATTTAACAACT
36054 AACTATATAATT
1 AACTATATAATT
36066 TATTTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
43 2 0.04
44 43 0.93
45 1 0.02
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (44 bp):
AACTATATAATTAAAATTAATGCAAAACTTAAAATTTAACAACT
Found at i:45463 original size:19 final size:19
Alignment explanation
Indices: 45439--45489 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
45429 ACCAACAAAA
45439 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
45458 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
45477 TCGCAATGCGATC
1 TCGCAATGCGATC
45490 TCCATTATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (19 bp):
TCGCAATGCGATCGCTAAT
Found at i:45605 original size:20 final size:21
Alignment explanation
Indices: 45580--45631 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
45570 TTTTCCCAAT
*
45580 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
45600 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
45621 TCGCAATGCGA
1 TCGCAATGCGA
45632 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:45645 original size:20 final size:20
Alignment explanation
Indices: 45620--45754 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
45610 AATTGGGAAA
45620 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
45640 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
45660 ATCGCAGTGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
45681 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
45701 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
45721 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
45741 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
45755 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:45664 original size:61 final size:61
Alignment explanation
Indices: 45617--45748 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
45607 GCGAATTGGG
* * * * **
45617 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAGTGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
45678 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
45739 ATAATCGCAA
1 AAAATCGCAA
45749 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:45950 original size:22 final size:22
Alignment explanation
Indices: 45922--45965 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
45912 CACTCTCTCA
45922 CCCATCTCCGACAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
* *
45944 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
45966 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:46280 original size:20 final size:20
Alignment explanation
Indices: 46226--46284 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
46216 GCGATTCTCT
**
46226 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
46246 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
46266 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
46285 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:46475 original size:25 final size:24
Alignment explanation
Indices: 46421--46475 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
46411 TGTTTATTAT
* *
46421 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
46445 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
46471 TGTTT
1 TGTTT
46476 ATTATTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:47625 original size:18 final size:18
Alignment explanation
Indices: 47604--47648 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
47594 TCCACTTCGG
*
47604 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
47622 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
47640 GAGCCATCA
1 GAGCCATCA
47649 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:48158 original size:20 final size:21
Alignment explanation
Indices: 48135--48190 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
48125 TGCAACACGA
48135 AAATGACTATCGCAACGTG-G
1 AAATGACTATCGCAACGTGCG
*
48155 AAATGGCTATCGCAA--TGCG
1 AAATGACTATCGCAACGTGCG
**
48174 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
48191 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (21 bp):
AAATGACTATCGCAACGTGCG
Found at i:48217 original size:19 final size:19
Alignment explanation
Indices: 48163--48226 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
48153 GGAAATGGCT
48163 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
48182 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
48196 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
48215 ATCGCAATGCGA
1 ATCGCAATGCGA
48227 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:48261 original size:14 final size:14
Alignment explanation
Indices: 48238--48295 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
48228 TTGTGTTTCA
48238 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
48252 CGTTGTGATTTCATTT
1 CGTTGCGATTT--TGT
48268 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
48284 CGTTGCGATTTT
1 CGTTGCGATTTT
48296 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:48276 original size:32 final size:33
Alignment explanation
Indices: 48240--48311 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
48230 GTGTTTCACG
*
48240 TTGCGATTTTGTCGTTGTGA-TTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
48272 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
48305 TTGCGAT
1 TTGCGAT
48312 AGCCATTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 19 0.50
33 19 0.50
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:48330 original size:20 final size:19
Alignment explanation
Indices: 48296--48351 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
48286 TTGCGATTTT
*
48296 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
48315 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
48335 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
48352 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:50365 original size:20 final size:20
Alignment explanation
Indices: 50340--50378 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
50330 ATATTGAAGG
50340 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
50360 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
50379 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:50390 original size:14 final size:14
Alignment explanation
Indices: 50371--50424 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
50361 AAAACTGACT
*
50371 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
50385 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
50404 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
50418 ATCGCAA
1 ATCGCAA
50425 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:50408 original size:19 final size:17
Alignment explanation
Indices: 50384--50429 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
50374 GCAACGAGAG
50384 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
50403 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
50417 AATCGCAATGCGA
1 AATCGCAATGCGA
50430 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:50447 original size:19 final size:19
Alignment explanation
Indices: 50419--50471 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
50409 AACGAGAAAA
*
50419 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
50438 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
50457 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
50472 GTCGTTGCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:50498 original size:19 final size:20
Alignment explanation
Indices: 50474--50523 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
50464 GCGATTTTGT
50474 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
50493 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
50513 CGTTGCGATAG
1 CGTTGCGATAG
50524 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:51761 original size:12 final size:12
Alignment explanation
Indices: 51744--51768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51734 ATATAATCCT
51744 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51756 GAAGAAGAAAAA
1 GAAGAAGAAAAA
51768 G
1 G
51769 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:54101 original size:33 final size:33
Alignment explanation
Indices: 54059--54185 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
54049 GGAAATTACT
*
54059 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
54092 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
54124 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
54158 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
54186 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:54166 original size:66 final size:66
Alignment explanation
Indices: 54060--54192 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
54050 GAAATTACTA
* *
54060 TCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
54125 T
66 T
*
54126 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
54191 T
66 T
54192 T
1 T
54193 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:54236 original size:33 final size:33
Alignment explanation
Indices: 54185--54274 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
54175 AAATCGCAAC
* * *
54185 GCGAATTTAATTTCGCGTTGTGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
54218 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
54251 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
54275 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:54238 original size:19 final size:19
Alignment explanation
Indices: 54214--54274 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
54204 GTGATTCTCT
54214 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
54233 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
54247 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
54266 CATTGCGAT
1 CGTTGCGAT
54275 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:54252 original size:14 final size:14
Alignment explanation
Indices: 54200--54256 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
54190 TTTAATTTCG
*
54200 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
54214 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
54233 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
54247 CGTTGCGATT
1 CGTTGCGATT
54257 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:54400 original size:14 final size:14
Alignment explanation
Indices: 54381--54417 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54371 CATCAATTAA
54381 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
54395 ACAAATCACCTTTT
1 ACAAATCAACTTTT
54409 ACAAATCAA
1 ACAAATCAA
54418 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:55831 original size:42 final size:41
Alignment explanation
Indices: 55772--55974 Score: 158
Period size: 42 Copynumber: 4.8 Consensus size: 41
55762 GTGAATCGGG
* *
55772 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGATAGTGGC
* * *
55814 CTCTTGAACGGTGGGAGGGGATTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGATAGTGGC
* * * * * * *
55856 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGATAGTGGC
* *
55898 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGATAGTGGC
* * * * *
55940 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGA
55975 CAGGCGAGTC
Statistics
Matches: 123, Mismatches: 30, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 103 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGATAGTGGC
Found at i:55913 original size:84 final size:84
Alignment explanation
Indices: 55802--55977 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
55792 CCTCTTCAAC
* * *
55802 GATGATAGTGGCCTCTTGAACGGTGGGAGGGGATTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
55867 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
55886 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
55951 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
55970 GATGACAG
1 GATGACAG
55978 GCGAGTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:56255 original size:17 final size:17
Alignment explanation
Indices: 56233--56265 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
56223 ATACTAACTT
56233 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
56250 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
56266 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:56375 original size:91 final size:90
Alignment explanation
Indices: 56194--56380 Score: 286
Period size: 91 Copynumber: 2.0 Consensus size: 90
56184 ATATTTCAAA
*
56194 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
56259 ACAGAATTGGCAGCAACCGAATAAATTT
63 ACAGAATTGGCAGCAACCGAATAAATTT
*
56287 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAA
* *
56351 TAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
56378 ACT
1 ACT
56381 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.45
93 21 0.24
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAACA
GAATTGGCAGCAACCGAATAAATTT
Found at i:56624 original size:63 final size:63
Alignment explanation
Indices: 56547--56677 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
56537 TAAAGTAGAC
56547 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
*
56610 ACCTCCACATGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
56673 ACCTC
1 ACCTC
56678 ATCACGTAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:58097 original size:19 final size:19
Alignment explanation
Indices: 58047--58139 Score: 97
Period size: 19 Copynumber: 5.1 Consensus size: 19
58037 TCTTTTGGTT
* *
58047 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGC
*
58066 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
58086 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
58103 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
58119 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
58138 GA
1 GA
58140 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:58114 original size:33 final size:33
Alignment explanation
Indices: 58072--58134 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
58062 ACGAGATAAT
58072 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
58105 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
58135 TGCGATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:58157 original size:19 final size:19
Alignment explanation
Indices: 58135--58179 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
58125 AAAATCGCAA
*
58135 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* * *
58154 TGCGTTTTTTATTTTGCGT
1 TGCGATTTTGATTTCGCGT
58173 TGCGATT
1 TGCGATT
58180 CTCTCGTTGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.13, G:0.27, T:0.53
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:58756 original size:20 final size:20
Alignment explanation
Indices: 58731--58783 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
58721 ACGCTATGTA
58731 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
58751 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
58771 TATCTCGTTGCGA
1 AATCGCGTTGCGA
58784 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:58817 original size:20 final size:20
Alignment explanation
Indices: 58792--58845 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
58782 GATTTTGTAT
58792 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
58812 TATCGCATTGTGATAGTCAG
1 TATCGCATTGCGATAGTAAG
58832 TATCGCATTGCGAT
1 TATCGCATTGCGAT
58846 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:58830 original size:61 final size:61
Alignment explanation
Indices: 58732--58848 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
58722 CGCTATGTAA
* * * * *
58732 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
58793 ATCGCATTGCGATAGTAAGTATCGCATTGTGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
58849 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:58864 original size:61 final size:61
Alignment explanation
Indices: 58732--58866 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
58722 CGCTATGTAA
* * * * * ** *
58732 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
58793 ATCGCATTGCGATAGTAAGTATCGCATTGTGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
58855 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
58867 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:71693 original size:30 final size:30
Alignment explanation
Indices: 71659--71719 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
71649 AATTAACAGT
*
71659 ATAATTAATA-TAATAATTTTTTTAATAATA
1 ATAATTAATATTAATAATGTTTTTAA-AATA
* *
71689 ATAATTTATATTAATTATGTTTTTAAAATA
1 ATAATTAATATTAATAATGTTTTTAAAATA
71719 A
1 A
71720 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATAATTAATATTAATAATGTTTTTAAAATA
Found at i:75771 original size:17 final size:18
Alignment explanation
Indices: 75749--75786 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
75739 TAATATTTTT
75749 AAAAATT-AAATTATATA
1 AAAAATTAAAATTATATA
*
75766 AAAAATTAAAATTTTATA
1 AAAAATTAAAATTATATA
75784 AAA
1 AAA
75787 TGATCACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTAAAATTATATA
Found at i:77054 original size:2 final size:2
Alignment explanation
Indices: 77047--77082 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
77037 TTTTTCAGAC
77047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77083 TGATAATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84784 original size:27 final size:27
Alignment explanation
Indices: 84754--84814 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
84744 AAACCAGGTG
* *
84754 AAGGCGGCGGAGACATCTGGTAATGGA
1 AAGGCGACGGAGACATCTGATAATGGA
* * *
84781 AAGGCGATGGCGGCATCTGATAATGGA
1 AAGGCGACGGAGACATCTGATAATGGA
84808 AAGGCGA
1 AAGGCGA
84815 TGGCGGCATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.39, T:0.15
Consensus pattern (27 bp):
AAGGCGACGGAGACATCTGATAATGGA
Found at i:84815 original size:27 final size:27
Alignment explanation
Indices: 84767--84824 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
84757 GCGGCGGAGA
*
84767 CATCTGGTAATGGAAAGGCGATGGCGG
1 CATCTGATAATGGAAAGGCGATGGCGG
84794 CATCTGATAATGGAAAGGCGATGGCGG
1 CATCTGATAATGGAAAGGCGATGGCGG
84821 CATC
1 CATC
84825 ATATATGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.36, T:0.19
Consensus pattern (27 bp):
CATCTGATAATGGAAAGGCGATGGCGG
Found at i:86534 original size:17 final size:18
Alignment explanation
Indices: 86514--86554 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
86504 AATTTATATT
*
86514 AGTAAAATA-TTAAATAA
1 AGTAAAATACCTAAATAA
86531 AGTAAAATACCTAAATAA
1 AGTAAAATACCTAAATAA
*
86549 ATTAAA
1 AGTAAA
86555 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (18 bp):
AGTAAAATACCTAAATAA
Found at i:86610 original size:10 final size:10
Alignment explanation
Indices: 86595--86625 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
86585 CCTTAAACGA
86595 GAGAGTATTT
1 GAGAGTATTT
86605 GAGAGTATTT
1 GAGAGTATTT
*
86615 GAGAGAATTT
1 GAGAGTATTT
86625 G
1 G
86626 GTGTGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (10 bp):
GAGAGTATTT
Found at i:97534 original size:54 final size:56
Alignment explanation
Indices: 97388--97543 Score: 262
Period size: 56 Copynumber: 2.8 Consensus size: 56
97378 AGGGGCACCG
* *
97388 AATCGAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAGGGTCCTTA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAAGGTCCTTA
*
97444 AATCAAATATATCTATCAGTTGTTGTCATTAATAAGTATAAAAATAAAGGTCCTTA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAAGGTCCTTA
*
97500 AATC-AA-ATATCTATCAGTTGTTCCCATTAATAAGTATAAAAATA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATA
97544 GAGCCCCGAA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
54 36 0.38
55 2 0.02
56 57 0.60
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (56 bp):
AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAAGGTCCTTA
Found at i:97564 original size:54 final size:55
Alignment explanation
Indices: 97388--97566 Score: 220
Period size: 56 Copynumber: 3.3 Consensus size: 55
97378 AGGGGCACCG
* * **
97388 AATCGAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAAGGGTCCTTA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAAT-AGAGTCCCGA
* * **
97444 AATCAAATATATCTATCAGTTGTTGTCATTAATAAGTATAAAAATAAAGGTCCTTA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAGA-GTCCCGA
* *
97500 AATC-AA-ATATCTATCAGTTGTTCCCATTAATAAGTATAAAAATAGAGCCCCGA
1 AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAGAGTCCCGA
*
97553 AGTC-AATATATCTA
1 AATCAAATATATCTA
97567 AAAATAAGGA
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
53 9 0.08
54 44 0.40
55 3 0.03
56 54 0.49
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (55 bp):
AATCAAATATATCTATCAGTTGTTGCCATTAATAAGTATAAAAATAGAGTCCCGA
Found at i:99756 original size:2 final size:2
Alignment explanation
Indices: 99749--99779 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
99739 TTATGCTTCC
99749 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 T
99780 TTTGTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103155 original size:182 final size:179
Alignment explanation
Indices: 102847--103492 Score: 809
Period size: 182 Copynumber: 3.6 Consensus size: 179
102837 CGATACAAAT
* * * * *
102847 TAAAAATGTATCGATCTATAGCAATATAACAGGTAAAAATATGATAAAACGGTGTC-ATTATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAAAGGTCTCGA-AATGAT
* ** * *
102911 AAAACCGATAAATCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAATGTCGACACTT
65 AAAA-CGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
* *
102976 TTGTAATTTAAAAGAGAATAAGTTATAGCGCCTAAAAGGTATCGATATTTTA
129 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTATCGATACTTTA
* *
103028 TAAAAATGTGTCGATCCATAGCAATATAACAGGTAATAATATGACAAAATAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAA-AGGTCTCGAAATGAT
103093 AAAACCGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
65 AAAA-CGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTT
*
103158 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCTTGAAAAGTATCGATACTTTA
129 TTGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTATCGATACTTTA
* * * * * *
103210 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAAGATGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAA-AGGTCTCGAAATGAT
* * *
103275 AAAACGGTAAAAAGATATCGGATATATTGAAAATGTCG-TAAATTAATATAAGTATCGACACTTT
65 AAAACGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
* * *
103339 CGTAATTTAAAAGAGAAGAAATTATAGCGCCTAAAAAGTGTCGATACTTTA
130 TGTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTATCGATACTTTA
* * * * * ** *
103390 -AGAAAATATATCGATCCATAACAATATAATAGGTAAAAACATGATAAACCGGTATCGAAATG--
1 TA-AAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAAAGGTCTCGAAATGAT
* ** *
103452 ACAACGGTAAAGCGCTACC-GATTATGTTGAAAGTGTCGATA
65 AAAACGGTAAAAAGCTACCGGA-TATATTGAAAGTGTCGATA
103493 CTTTAATAAG
Statistics
Matches: 408, Mismatches: 51, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
176 2 0.00
177 28 0.07
178 2 0.00
179 11 0.03
180 108 0.26
181 76 0.19
182 176 0.43
183 5 0.01
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (179 bp):
TAAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAAAGGTCTCGAAATGATA
AAACGGTAAAAAGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTT
GTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTATCGATACTTTA
Done.