Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000523.1 Hibiscus syriacus cultivar Beakdansim tig00001005_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: 88449
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1493 original size:29 final size:29
Alignment explanation
Indices: 1461--1523 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
1451 TTATACCTTT
1461 GAAACAAATAAT-ATTAACTGACTAAAATA
1 GAAACAAATAATAATTAACTGAC-AAAATA
1490 GAAACAAATAATAATTAACTGACAAAATA
1 GAAACAAATAATAATTAACTGACAAAATA
1519 GAAAC
1 GAAAC
1524 TATGCATAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 23 0.70
30 10 0.30
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (29 bp):
GAAACAAATAATAATTAACTGACAAAATA
Found at i:8958 original size:20 final size:20
Alignment explanation
Indices: 8933--8973 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8923 TTTAATTTTA
**
8933 AATATTAAAAATTTAAAAAT
1 AATATTAAAAACATAAAAAT
*
8953 AATATTATAAACATAAAAAT
1 AATATTAAAAACATAAAAAT
8973 A
1 A
8974 TAGCATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATTAAAAACATAAAAAT
Found at i:24089 original size:44 final size:44
Alignment explanation
Indices: 24035--24122 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
24025 GGGATTGATG
* *
24035 ATTGAGCTAATTGTATGTTCAATTTTGGGTTCAATCAATAATCA
1 ATTGAACTAATTGAATGTTCAATTTTGGGTTCAATCAATAATCA
24079 ATTGAACTAATTGAATGTTCAATTTTGGGTTCAATCAATAATCA
1 ATTGAACTAATTGAATGTTCAATTTTGGGTTCAATCAATAATCA
24123 TTGGTTTCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (44 bp):
ATTGAACTAATTGAATGTTCAATTTTGGGTTCAATCAATAATCA
Found at i:36978 original size:21 final size:20
Alignment explanation
Indices: 36938--36984 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
36928 GATTATGTGT
*
36938 TATGAACTTTGATAAGTGAA
1 TATGAACTTCGATAAGTGAA
*
36958 TATGAACTTCGAATCAGTGAA
1 TATGAACTTCG-ATAAGTGAA
*
36979 TGTGAA
1 TATGAA
36985 TATACTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (20 bp):
TATGAACTTCGATAAGTGAA
Found at i:41000 original size:18 final size:19
Alignment explanation
Indices: 40977--41017 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
40967 ATATAAAAAT
* *
40977 GGTATCGGTACC-TAAGGG
1 GGTATCGATACCATAAGAG
40995 GGTATCGATACCATAAGAG
1 GGTATCGATACCATAAGAG
41014 GGTA
1 GGTA
41018 GTATCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (19 bp):
GGTATCGATACCATAAGAG
Found at i:42405 original size:30 final size:30
Alignment explanation
Indices: 42369--42440 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
42359 CCCGAAGGAC
*
42369 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
42399 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
42429 CTGTCCATAGGT
1 CTATCCAGAGGT
42441 TCAGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:42532 original size:32 final size:31
Alignment explanation
Indices: 42428--42550 Score: 117
Period size: 31 Copynumber: 3.9 Consensus size: 31
42418 ATCCTCGGCA
* * *
42428 ACTGTCCATAGGTTCAGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGAAG-ACATAGGTAAT
***
42459 ACTGTCCATATGTTCATTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGAAG-ACATAGGTAAT
42490 ACTGTCCATATGTGT-CGAAAGACATAGGTAAT
1 ACTGTCCATATGT-TCCG-AAGACATAGGTAAT
* *
42522 TCTGTCCATATGTTCCGTAGACATAGGTA
1 ACTGTCCATATGTTCCGAAGACATAGGTA
42551 TACCCTCGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
30 1 0.01
31 58 0.74
32 19 0.24
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
ACTGTCCATATGTTCCGAAGACATAGGTAAT
Found at i:44753 original size:21 final size:21
Alignment explanation
Indices: 44727--44800 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
44717 GGAATATATT
44727 TGGTCATTCGGGACATCTATG
1 TGGTCATTCGGGACATCTATG
44748 TGGTCATTCGGGACATCTATG
1 TGGTCATTCGGGACATCTATG
*
44769 TGGTCATTCGGGACATATATG
1 TGGTCATTCGGGACATCTATG
44790 TGGTCATTCGG
1 TGGTCATTCGG
44801 AACAAATTCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.19, C:0.18, G:0.30, T:0.34
Consensus pattern (21 bp):
TGGTCATTCGGGACATCTATG
Found at i:47581 original size:30 final size:30
Alignment explanation
Indices: 47545--47604 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
47535 AAGGATGCAC
47545 GCACCGAATATACATAATTTCAATGGGTTG
1 GCACCGAATATACATAATTTCAATGGGTTG
* **
47575 GCACCGAATGTGTATAATTTCAATGGGTTG
1 GCACCGAATATACATAATTTCAATGGGTTG
47605 TCAATTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (30 bp):
GCACCGAATATACATAATTTCAATGGGTTG
Found at i:52076 original size:30 final size:30
Alignment explanation
Indices: 52030--52092 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
52020 AAGGATGCAC
52030 GCACCGAATATGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGTTG
* *
52060 GCACTGAATGTGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGTTG
52090 GCA
1 GCA
52093 ATTGTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (30 bp):
GCACCGAATATGCATAATTTCAATGGGTTG
Found at i:52799 original size:26 final size:25
Alignment explanation
Indices: 52750--52799 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
52740 ATACTTATTT
*
52750 TGATCAAAAAATACTTTTAAGTATG
1 TGATCAAAAAATAATTTTAAGTATG
* *
52775 TGATCAAAATGATAATTTTAGGTAT
1 TGATCAAAA-AATAATTTTAAGTAT
52800 TTATTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (25 bp):
TGATCAAAAAATAATTTTAAGTATG
Found at i:54338 original size:20 final size:20
Alignment explanation
Indices: 54244--54612 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
54234 GATTTTCCAT
* ** *
54244 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
54264 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
54284 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
54304 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
54324 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
54344 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
54364 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
54384 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
54404 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
54424 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
54444 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
54464 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
54484 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
54504 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
54524 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
54544 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
54564 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
54584 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
54604 AATCACAAC
1 AATCGCAAC
54613 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:55526 original size:12 final size:12
Alignment explanation
Indices: 55509--55533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55499 ATATAATCCT
55509 GAAGAAGAAAAA
1 GAAGAAGAAAAA
55521 GAAGAAGAAAAA
1 GAAGAAGAAAAA
55533 G
1 G
55534 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:57826 original size:19 final size:19
Alignment explanation
Indices: 57804--58102 Score: 304
Period size: 19 Copynumber: 17.4 Consensus size: 19
57794 CGGAAAATAC
*
57804 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57823 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
57837 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
57857 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
57871 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
57889 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57908 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
57922 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
57941 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
57960 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
57974 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
57993 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58012 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
58026 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
58044 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
58058 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58077 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
58095 AATCGCAA
1 AATCGCAA
58103 CGAGATAATC
Statistics
Matches: 239, Mismatches: 10, Indels: 63
0.77 0.03 0.20
Matches are distributed among these distances:
14 56 0.23
15 3 0.01
16 26 0.11
17 15 0.06
18 37 0.15
19 89 0.37
20 13 0.05
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:57929 original size:33 final size:33
Alignment explanation
Indices: 57871--58102 Score: 224
Period size: 33 Copynumber: 6.7 Consensus size: 33
57861 GCAACGAGAG
57871 AATCGCAATGCGAAATGAAATCGCAATGCGAAATGAA
1 AATCGCAA--CGAAA-G-AATCGCAATGCGAAATGAA
* *
57908 AATCGCAACGAGATAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
*
57941 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--
1 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
57974 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG-AA--AGAATCGCAATGCGAAATGAA
58012 AATCGCAACGAAAGAATCGCAATGCGAAATG-A
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
58044 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAAAGAATCGCAATGCGAAATGAA
58077 AATCGCAATGCGAAATGAAATCGCAA
1 AATCGCAA--CGAAA-G-AATCGCAA
58103 CGAGATAATC
Statistics
Matches: 169, Mismatches: 8, Indels: 36
0.79 0.04 0.17
Matches are distributed among these distances:
32 32 0.19
33 74 0.44
34 2 0.01
35 20 0.12
36 9 0.05
37 16 0.09
38 16 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (33 bp):
AATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:57944 original size:52 final size:51
Alignment explanation
Indices: 57836--58102 Score: 382
Period size: 52 Copynumber: 5.2 Consensus size: 51
57826 CCCAACATGA
57836 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
*
57888 AAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
* *
57939 AAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTA
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAA-TG
*
57992 AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
*
58043 AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATG
58094 AAATCGCAA
1 AAATCGCAA
58103 CGAGATAATC
Statistics
Matches: 200, Mismatches: 8, Indels: 15
0.90 0.04 0.07
Matches are distributed among these distances:
46 8 0.04
48 3 0.01
49 5 0.03
50 1 0.00
51 75 0.38
52 107 0.54
53 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (51 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
Found at i:58239 original size:19 final size:19
Alignment explanation
Indices: 58130--58231 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
58120 GAAATTATAA
58130 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
58149 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
58169 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
58185 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
58202 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
58221 CGCATTGCGAT
1 CGCATTGCGAT
58232 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:58364 original size:13 final size:14
Alignment explanation
Indices: 58337--58372 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
58327 CATCAATTAC
58337 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
58351 ACAAATCATC-TTT
1 ACAAATCAACTTTT
58364 ACAAATCAA
1 ACAAATCAA
58373 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:60366 original size:14 final size:14
Alignment explanation
Indices: 60347--60403 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
60337 GCGAAATGAA
*
60347 AATCGCAACGACAG
1 AATCGCAACGAAAG
60361 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
60378 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
60394 AATCGCAACG
1 AATCGCAACG
60404 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:60374 original size:33 final size:33
Alignment explanation
Indices: 60328--60420 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
60318 GCGAAACCAA
*
60328 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
60361 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
60394 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
60421 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:60385 original size:19 final size:19
Alignment explanation
Indices: 60291--60425 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
60281 TAGTTTACTT
* *
60291 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
60311 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
60330 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
60349 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
60363 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
60382 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
60396 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
60415 TCGCAATGCGA
1 TCGCAACGCGA
60426 TTTTGATTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:60443 original size:19 final size:19
Alignment explanation
Indices: 60421--60549 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
60411 AAAATCGCAA
60421 TGCGATTTTGATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
60440 TGCGATCTTG---T--CGT
1 TGCGATTTTGATTTCGCGT
*
60454 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
60473 TGCGATTCTG---T--CGT
1 TGCGATTTTGATTTCGCGT
*
60487 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
60506 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
60525 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTTGA-TTTCGCGT
60545 TGCGA
1 TGCGA
60550 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 23 0.26
16 2 0.02
17 2 0.02
19 50 0.56
20 12 0.13
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:60463 original size:33 final size:33
Alignment explanation
Indices: 60421--60512 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
60411 AAAATCGCAA
60421 TGCGATTTTGATTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGATTTCGCGTTGCGATTC-TGTCGT
*
60454 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGATTTCGCGTTGCGATTCTGTCGT
*
60487 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGATTTCGCGTTGCGATT
60513 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGATTTCGCGTTGCGATTCTGTCGT
Found at i:60827 original size:93 final size:93
Alignment explanation
Indices: 60581--61046 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
60571 GCAAATTGAA
60581 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
60646 GCAGAATTGGCAGCAACCGAAC-AATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
60673 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
60738 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
60766 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
60831 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
60859 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
60923 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
60951 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
61016 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
61044 ACT
1 ACT
61047 AAGCAATCTA
Statistics
Matches: 371, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 179 0.48
93 192 0.52
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:60898 original size:185 final size:186
Alignment explanation
Indices: 60581--61046 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
60571 GCAAATTGAA
60581 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
60646 GCAGAATTGGCAGCAACCGAAC-AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
60710 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
60766 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
60831 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
60895 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
60951 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
61016 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
61047 AAGCAATCTA
Statistics
Matches: 279, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 241 0.86
186 38 0.14
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:62769 original size:14 final size:14
Alignment explanation
Indices: 62750--62839 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
62740 TTGAAATGAA
62750 AATCGCAACGAGAG
1 AATCGCAACGAGAG
62764 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
62781 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
62797 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
62816 AATCGCAACGAGAG
1 AATCGCAACGAGAG
62830 AATCGCAACG
1 AATCGCAACG
62840 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:62787 original size:33 final size:33
Alignment explanation
Indices: 62742--62856 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
62732 TCTTTTGGTT
62742 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
62775 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
62808 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
62841 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
62857 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:62788 original size:19 final size:18
Alignment explanation
Indices: 62749--62861 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
62739 GTTGAAATGA
62749 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
62764 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
62781 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
62797 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
62814 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
62830 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
62847 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
62862 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:62892 original size:14 final size:14
Alignment explanation
Indices: 62873--62927 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
62863 TTTGGTTTCG
62873 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
62887 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
62906 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
62920 CGTTGCGA
1 CGTTGCGA
62928 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:62905 original size:33 final size:33
Alignment explanation
Indices: 62857--62927 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
62847 AAAATCGCAA
**
62857 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
62890 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
62923 TGCGA
1 TGCGA
62928 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:62935 original size:33 final size:33
Alignment explanation
Indices: 62868--62949 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
62858 GCGATTTTGG
***
62868 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
62901 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
62934 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
62950 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:62954 original size:20 final size:20
Alignment explanation
Indices: 62880--62968 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
62870 TCGCGTTGCG
62880 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
62900 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
62913 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
62933 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
62953 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
62969 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:63090 original size:33 final size:33
Alignment explanation
Indices: 63048--63118 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
63038 AATACTAACT
*
63048 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
63081 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
63114 TGAAA
1 TGAAA
63119 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:63352 original size:22 final size:22
Alignment explanation
Indices: 63300--63354 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
63290 TGGTTGTGAG
**
63300 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
63322 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
63344 GGATTTCTTCG
1 GGATTTCTTCG
63355 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:63525 original size:20 final size:20
Alignment explanation
Indices: 63500--63692 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
63490 CTTTAAATAT
63500 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
63520 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
63542 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
63561 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
63581 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
63601 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
63621 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
63641 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
63661 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
63681 CGCGTTGCGATT
1 CGCGTTGCGATT
63693 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:63687 original size:60 final size:60
Alignment explanation
Indices: 63500--63692 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
63490 CTTTAAATAT
**
63500 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
63561 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
63621 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
63681 CGCGTTGCGATT
1 CGCGTTGCGATT
63693 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:63773 original size:20 final size:20
Alignment explanation
Indices: 63748--63799 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
63738 AAGAATCGCG
*
63748 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
63768 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
63788 TTGCGATTCTGG
1 TTGCGATTCTGG
63800 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:64949 original size:21 final size:21
Alignment explanation
Indices: 64925--65040 Score: 132
Period size: 21 Copynumber: 5.6 Consensus size: 21
64915 TTTGGAATAA
*
64925 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
64946 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
64966 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
64987 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
65008 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
65029 ATCGCATTGCGA
1 ATCGCAATGCGA
65041 TTTACATATT
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
20 17 0.21
21 64 0.79
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:65083 original size:21 final size:21
Alignment explanation
Indices: 65049--65206 Score: 171
Period size: 21 Copynumber: 7.6 Consensus size: 21
65039 GATTTACATA
*
65049 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
65070 TTCACATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
65091 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
65112 TTCGCGTTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* * *
65132 TATCACATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
65153 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
65174 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
65195 TTCG-AGTTGCGA
1 TTCGCA-TTGCGA
65207 ATCTGGAAAC
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
20 16 0.14
21 98 0.85
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:66923 original size:19 final size:19
Alignment explanation
Indices: 66899--66940 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
66889 TAGGTCTCCA
66899 GGAGCACACGGCGACCTAT
1 GGAGCACACGGCGACCTAT
***
66918 GGAGCATTTGGCGACCTAT
1 GGAGCACACGGCGACCTAT
66937 GGAG
1 GGAG
66941 TTGCAATAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.17
Consensus pattern (19 bp):
GGAGCACACGGCGACCTAT
Found at i:68120 original size:104 final size:104
Alignment explanation
Indices: 67939--68170 Score: 365
Period size: 104 Copynumber: 2.2 Consensus size: 104
67929 AAGTCGTCGG
*
67939 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATCACTGTT
1 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATAACTGTT
*
68004 ACTTATGGGAAATAAAGGAAACCAATGCTTGAACATTTC
66 ACTTATGAGAAATAAAGGAAACCAATGCTTGAACATTTC
* * *
68043 GAGGACTTGGTGACCTATGGAGGTTTCGACTAAAATCCTAATTACCGATTTAGGTAATAACTGTT
1 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATAACTGTT
* ** * *
68108 ATTTATGAGAAATCTAGGAAACCAATGCTTGAACGTTTG
66 ACTTATGAGAAATAAAGGAAACCAATGCTTGAACATTTC
*
68147 GAGGACTTGGCAACCTATGGAGGT
1 GAGGACTTGGCGACCTATGGAGGT
68171 CGCCTAGAGT
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 116 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (104 bp):
GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATAACTGTT
ACTTATGAGAAATAAAGGAAACCAATGCTTGAACATTTC
Found at i:73144 original size:21 final size:21
Alignment explanation
Indices: 73115--73167 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
73105 ATTCTGACTA
73115 TCGCATTGCGATCTTCCAAAT
1 TCGCATTGCGATCTTCCAAAT
* * *
73136 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATCTTCCAAAT
*
73157 TCGCAATGCGA
1 TCGCATTGCGA
73168 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATCTTCCAAAT
Found at i:73182 original size:20 final size:20
Alignment explanation
Indices: 73157--73217 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
73147 TTTTCCTAAT
73157 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
73177 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
73197 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
73217 T
1 T
73218 TGTAATTCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:73252 original size:20 final size:20
Alignment explanation
Indices: 73229--73302 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
73219 GTAATTCGAA
* *
73229 TCTGACTATTGCAACGAAAT
1 TCTGACTATCGCAACGAGAT
73249 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
73269 TCTGACTATCGCAAC-ACGAT
1 TCTGACTATCGCAACGA-GAT
* *
73289 TATGACTATTGCAA
1 TCTGACTATCGCAA
73303 TACTGAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:74161 original size:24 final size:24
Alignment explanation
Indices: 74134--74192 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
74124 AGTCAGTATT
74134 CGAAATTTGATCTCGGTCAATACC
1 CGAAATTTGATCTCGGTCAATACC
* *
74158 CGAACTTTGATCTTGGTCAATACC
1 CGAAATTTGATCTCGGTCAATACC
*
74182 CGAATTTTGAT
1 CGAAATTTGAT
74193 GATGAAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTCGGTCAATACC
Found at i:74306 original size:3 final size:3
Alignment explanation
Indices: 74298--74327 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
74288 ATATAACCCT
74298 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
74328 ATCCCCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:76567 original size:20 final size:20
Alignment explanation
Indices: 76542--76635 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
76532 GACATTCATT
76542 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
76562 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
76582 TGACTATCACAACGTGGAAA
1 TGACTATCGCAACGCGGAAA
76602 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
76622 TGACTATCGCAACG
1 TGACTATCGCAACG
76636 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:76871 original size:14 final size:14
Alignment explanation
Indices: 76852--76902 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
76842 CATCAATTAA
76852 ACAAATCAACATTT
1 ACAAATCAACATTT
76866 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
76880 ACAAATCATCTTTT
1 ACAAATCAACATTT
76894 ACAAATCAA
1 ACAAATCAA
76903 TTAAACAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:78389 original size:42 final size:42
Alignment explanation
Indices: 78282--78393 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
78272 TATAAAATGT
* * * *
78282 TGGGAG-GGACCTCTTCAACGACGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
78324 TGGGAGGGGACTCTTGATGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
78366 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
78394 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:78894 original size:20 final size:20
Alignment explanation
Indices: 78871--79015 Score: 131
Period size: 20 Copynumber: 7.5 Consensus size: 20
78861 GAAACTTAAA
78871 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
78891 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* * ** *
78911 ATTGCAATGCGAATTTGACA
1 ATCGCAACGCGAAAATGACT
*
78931 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
78945 ATCGCAATGCGCGAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
78967 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
78987 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
79007 ATCGCAACG
1 ATCGCAACG
79016 AGAGAATCGC
Statistics
Matches: 100, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
14 7 0.07
16 2 0.02
17 1 0.01
18 4 0.04
19 2 0.02
20 77 0.77
22 7 0.07
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:78967 original size:76 final size:76
Alignment explanation
Indices: 78870--79031 Score: 274
Period size: 76 Copynumber: 2.2 Consensus size: 76
78860 TGAAACTTAA
* *
78870 AATCGCAA--CGCGAAAATGACTATCGCAACACGGAAATGACTATTGCAATGCGAATTTGACAAT
1 AATCGCAATGCGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACAAT
78933 CGCAACGAGAG
66 CGCAACGAGAG
* *
78944 AATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCGAATTTGACTAT
1 AATCGCAATGCGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACAAT
79009 CGCAACGAGAG
66 CGCAACGAGAG
79020 AATCGCAATGCG
1 AATCGCAATGCG
79032 ATTTTCATTT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 8 0.10
76 74 0.90
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (76 bp):
AATCGCAATGCGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACAAT
CGCAACGAGAG
Found at i:79065 original size:20 final size:20
Alignment explanation
Indices: 79040--79112 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
79030 CGATTTTCAT
*
79040 TTCGCATTACGATAGTCAAA
1 TTCGCATTGCGATAGTCAAA
**
79060 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCAAA
**
79080 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCAAA
*
79100 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
79113 TTTGTTGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAA
Found at i:79094 original size:40 final size:39
Alignment explanation
Indices: 79022--79112 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 39
79012 AACGAGAGAA
* **
79022 TCGCAATGCGATTTTCATTTCGCATTACGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTACGATAGTCAAAT
* **
79061 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTACGATAGTCAAAT
*
79101 TCGCGTTGCGAT
1 TCGCATTGCGAT
79113 TTTGTTGTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 14 0.32
40 30 0.68
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (39 bp):
TCGCATTGCGATAGTCATTTCGCATTACGATAGTCAAAT
Found at i:79122 original size:14 final size:14
Alignment explanation
Indices: 79097--79154 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
79087 TGCGATAGTC
*
79097 ATTTTCGCGTTGCG
1 ATTTTCTCGTTGCG
* * *
79111 ATTTTGTTGTTGTG
1 ATTTTCTCGTTGCG
79125 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
79139 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
79153 AT
1 AT
79155 AGTAAACTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.52
Consensus pattern (14 bp):
ATTTTCTCGTTGCG
Found at i:81053 original size:20 final size:20
Alignment explanation
Indices: 81030--81192 Score: 108
Period size: 20 Copynumber: 8.6 Consensus size: 20
81020 TCTGAAACTT
81030 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
81050 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
81070 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
81090 ACTATCGC-A-ACG-CAA-G
1 AAAATCGCAACACGAAAATG
*
81106 --AATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
81123 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
81143 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
81163 ACTATTGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
81182 AAAATCGCAAC
1 AAAATCGCAAC
81193 GACAGAATCG
Statistics
Matches: 113, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 5 0.04
17 1 0.01
18 2 0.02
19 23 0.20
20 76 0.67
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:81133 original size:53 final size:55
Alignment explanation
Indices: 81052--81193 Score: 162
Period size: 53 Copynumber: 2.5 Consensus size: 55
81042 CGAAAATGAA
* ** **
81052 AATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGC-AA-G
1 AATCGCAACGCG-AAATGAAAATCGCAACGCGAAAATGACTATCGCAACGCGAATG
*
81106 AATCGCAACGCGAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGCGAA--TG
*
81163 ACTATTGCAACGCGAAATGAAAATCGCAACG
1 A--ATCGCAACGCGAAATGAAAATCGCAACG
81194 ACAGAATCGC
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
53 33 0.45
54 13 0.18
57 2 0.03
59 26 0.35
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (55 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGCGAATG
Found at i:81152 original size:73 final size:74
Alignment explanation
Indices: 81032--81175 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 74
81022 TGAAACTTAA
81032 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
81097 CAACGCAAG
66 CAACGCAAG
* *
81106 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATTG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
81170 CAACGC
66 CAACGC
81176 GAAATGAAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 57 0.84
74 11 0.16
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (74 bp):
AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
CAACGCAAG
Found at i:81173 original size:93 final size:92
Alignment explanation
Indices: 81030--81204 Score: 244
Period size: 93 Copynumber: 1.9 Consensus size: 92
81020 TCTGAAACTT
* **
81030 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTAT
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAA-ATGAAAAT
81095 CGCAACG-CAAGAATCGCAACGCGAAATG
65 CGCAACGAC-AGAATCGCAACGCGAAATG
** * ** *
81123 AAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATTGCAACGCGAAATGAAAATC
1 AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGAAAATC
81188 GCAACGACAGAATCGCA
66 GCAACGACAGAATCGCA
81205 TTGCGATAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
92 21 0.29
93 51 0.71
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.15
Consensus pattern (92 bp):
AAAATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGAAAATC
GCAACGACAGAATCGCAACGCGAAATG
Found at i:81590 original size:22 final size:22
Alignment explanation
Indices: 81529--81594 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
81519 TAACCGTGAA
* ** *
81529 TGATTTCGCCGGAGATGAAGCC
1 TGATTTCGTCGGAGATGGGGAC
*
81551 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
81573 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
81595 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:81813 original size:20 final size:20
Alignment explanation
Indices: 81772--81838 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
81762 GCTATGTAAA
* *
81772 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACATAT
*
81792 TCACATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
81812 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
81832 TCGCATT
1 TCGCATT
81839 ACGAATTAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:82256 original size:28 final size:30
Alignment explanation
Indices: 82208--82278 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
82198 CCCTAAATTG
*
82208 TTTTTGAAATTTT-TAGGAATTT-AGGAGT
1 TTTTTGAAATTTTATAGAAATTTAAGGAGT
*
82236 TTTTTGAAATTTTAT-GAAATTTAAGGTGT
1 TTTTTGAAATTTTATAGAAATTTAAGGAGT
82265 TTTTT-AGAATTTTA
1 TTTTTGA-AATTTTA
82279 ATAATTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 20 0.53
29 18 0.47
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.54
Consensus pattern (30 bp):
TTTTTGAAATTTTATAGAAATTTAAGGAGT
Done.