Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004428.1 Hibiscus syriacus cultivar Beakdansim tig00009709_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: 92720
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4037 original size:45 final size:45
Alignment explanation
Indices: 3954--4046 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 45
3944 AAAAACATAA
* * *
3954 AAAGAAATAAATAATGTACCACACACAAATATAATCTTTAAATCT
1 AAAGAAACAAATAATGTACCACAAACAAATATAATCTTTAAATAT
* * * *
3999 AAAGAAACAAATAATGTA-CATCAAATAAATTTATTCTTTCAATAT
1 AAAGAAACAAATAATGTACCA-CAAACAAATATAATCTTTAAATAT
4044 AAA
1 AAA
4047 TACATATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 2 0.05
45 38 0.95
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (45 bp):
AAAGAAACAAATAATGTACCACAAACAAATATAATCTTTAAATAT
Found at i:5598 original size:24 final size:24
Alignment explanation
Indices: 5571--5620 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5561 GTGGTGGAGG
*
5571 GGGCTGCTGGGTTACTTGAAACGT
1 GGGCTACTGGGTTACTTGAAACGT
* **
5595 GGGCTATTGGGTTGTTTGAAACGT
1 GGGCTACTGGGTTACTTGAAACGT
5619 GG
1 GG
5621 AGAGGTTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.32
Consensus pattern (24 bp):
GGGCTACTGGGTTACTTGAAACGT
Found at i:10256 original size:33 final size:33
Alignment explanation
Indices: 10207--10276 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
10197 GTTTTGGGAG
* *
10207 AAGTGTCACATCTTTACAGAGCACAAGAGCCTT
1 AAGTGTCACATATTTACAGAACACAAGAGCCTT
* *
10240 AAGTTTCACATATTTACGGAACACAAGAGCCTT
1 AAGTGTCACATATTTACAGAACACAAGAGCCTT
10273 AAGT
1 AAGT
10277 ATCTCCTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (33 bp):
AAGTGTCACATATTTACAGAACACAAGAGCCTT
Found at i:21736 original size:21 final size:21
Alignment explanation
Indices: 21712--21752 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21702 TGCCACATAT
21712 TTATCCCGAAAGACCATATAA
1 TTATCCCGAAAGACCATATAA
** *
21733 TTATCTTGAATGACCATATA
1 TTATCCCGAAAGACCATATA
21753 GACCCTCGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (21 bp):
TTATCCCGAAAGACCATATAA
Found at i:21947 original size:14 final size:14
Alignment explanation
Indices: 21928--21957 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21918 ATATTCATAA
*
21928 AATATAACTTGAAT
1 AATATAAATTGAAT
21942 AATATAAATTGAAT
1 AATATAAATTGAAT
21956 AA
1 AA
21958 ATAGAATAAA
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:0.03, G:0.07, T:0.33
Consensus pattern (14 bp):
AATATAAATTGAAT
Found at i:22295 original size:20 final size:20
Alignment explanation
Indices: 22266--22337 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
22256 CATGGTTATA
*
22266 GGTATTGATACTACCCTAAT
1 GGTATCGATACTACCCTAAT
* *
22286 GGTATCGATACTACCATTCAAG
1 GGTATCGATACTACC-CT-AAT
*
22308 GGTATCGATAC--CTCCTCAT
1 GGTATCGATACTAC-CCTAAT
22327 GGTATCGATAC
1 GGTATCGATAC
22338 CGAAATAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 12 0.28
20 16 0.37
21 2 0.05
22 13 0.30
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (20 bp):
GGTATCGATACTACCCTAAT
Found at i:22379 original size:54 final size:54
Alignment explanation
Indices: 22302--22446 Score: 184
Period size: 54 Copynumber: 2.7 Consensus size: 54
22292 GATACTACCA
* *
22302 TTCAAGGGTATCGATACCTCCTCATGGTATCGATACCGAA-ATAACATTCGATGT
1 TTCAAGGGTATCGATACCACCTCAAGGTATCGATACC-AATATAACATTCGATGT
* * **
22356 TTCAAGGGTATCGATACCACCTCAAGGTACCGATACCAATCTGGCATTCGATGT
1 TTCAAGGGTATCGATACCACCTCAAGGTATCGATACCAATATAACATTCGATGT
* * *
22410 TTTAAGGGTATCGATATCATCCTTAAGGTATCGATAC
1 TTCAAGGGTATCGATACCA-CCTCAAGGTATCGATAC
22447 TACCCTTACG
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
53 2 0.03
54 62 0.78
55 15 0.19
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCACCTCAAGGTATCGATACCAATATAACATTCGATGT
Found at i:22453 original size:20 final size:21
Alignment explanation
Indices: 22411--22466 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
22401 ATTCGATGTT
*
22411 TTAAGGGTATCGATA-TCATCC
1 TTAA-GGTATCGATACTCACCC
22432 TTAAGGTATCGATACT-ACCC
1 TTAAGGTATCGATACTCACCC
* *
22452 TTACGGTATTGATAC
1 TTAAGGTATCGATAC
22467 CTCTATCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 26 0.84
21 5 0.16
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (21 bp):
TTAAGGTATCGATACTCACCC
Found at i:30581 original size:2 final size:2
Alignment explanation
Indices: 30574--30609 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30564 TCCCCCATAA
30574 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
30610 TGCAATTTGT
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:32713 original size:24 final size:24
Alignment explanation
Indices: 32686--32739 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
32676 ATCGCCTCTT
32686 CTTCGGCTTTAGCCTTTGCCATGG
1 CTTCGGCTTTAGCCTTTGCCATGG
32710 CTTCGGCTTTAGCCTTTGCCATGG
1 CTTCGGCTTTAGCCTTTGCCATGG
32734 CTTCGG
1 CTTCGG
32740 AATACGCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.07, C:0.30, G:0.26, T:0.37
Consensus pattern (24 bp):
CTTCGGCTTTAGCCTTTGCCATGG
Found at i:32748 original size:24 final size:24
Alignment explanation
Indices: 32686--32749 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
32676 ATCGCCTCTT
**
32686 CTTCGGCTTTAGCCTTTGCCATGG
1 CTTCGGCAATAGCCTTTGCCATGG
**
32710 CTTCGGCTTTAGCCTTTGCCATGG
1 CTTCGGCAATAGCCTTTGCCATGG
32734 CTTCGG-AATACGCCTT
1 CTTCGGCAATA-GCCTT
32750 CCTTCTTCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.05
24 35 0.95
ACGTcount: A:0.11, C:0.30, G:0.23, T:0.36
Consensus pattern (24 bp):
CTTCGGCAATAGCCTTTGCCATGG
Found at i:36038 original size:21 final size:21
Alignment explanation
Indices: 35997--36040 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35987 GTAATCTATC
*
35997 ATATTGATTTGACAGTTCACG
1 ATATTGATTTGACAGTACACG
*
36018 ATATT-ATTGTGATAGTACACG
1 ATATTGATT-TGACAGTACACG
36039 AT
1 AT
36041 GAACAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (21 bp):
ATATTGATTTGACAGTACACG
Found at i:36128 original size:18 final size:19
Alignment explanation
Indices: 36110--36200 Score: 71
Period size: 18 Copynumber: 4.5 Consensus size: 19
36100 ATATAAAATA
36110 TAAATAATTATTAAGATAT
1 TAAATAATTATTAAGATAT
36129 TAAA-AATTATTAAGAAATTAT
1 TAAATAATTATTAAG--A-TAT
* *
36150 TAAAATTTAA-AATATAAAATA-
1 T-AAA--TAATTAT-TAAGATAT
36171 TAAATAATTATTAAGATAT
1 TAAATAATTATTAAGATAT
36190 TAAATATATTA
1 TAAATA-ATTA
36201 AATATAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
18 19 0.33
19 12 0.21
20 8 0.14
21 5 0.09
22 5 0.09
23 1 0.02
24 2 0.04
25 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TAAATAATTATTAAGATAT
Found at i:36150 original size:21 final size:18
Alignment explanation
Indices: 36110--36211 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 18
36100 ATATAAAATA
36110 TAAATAATTATTAAGATAT
1 TAAA-AATTATTAAGATAT
36129 TAAAAATTATTAAGAAATTAT
1 TAAAAATTATTAAG--A-TAT
* *
36150 TAAAATTTAAAATATAAAATA-
1 TAAAAATT---AT-TAAGATAT
36171 TAAATAATTATTAAGATAT
1 TAAA-AATTATTAAGATAT
*
36190 TAAATA-TATTAA-ATA-
1 TAAAAATTATTAAGATAT
36205 TAAAAAT
1 TAAAAAT
36212 ACTAAAAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
15 5 0.07
16 3 0.04
17 6 0.09
18 17 0.25
19 10 0.15
20 1 0.01
21 14 0.21
22 5 0.07
23 1 0.01
24 2 0.03
25 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAAATTATTAAGATAT
Found at i:36234 original size:24 final size:24
Alignment explanation
Indices: 36156--36234 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
36146 TTATTAAAAT
*
36156 TTAAAATA-TAAAATATAAATAATTA
1 TTAAAATACT-AAATA-AATTAATTA
* * * *
36181 TTAAGATATTAAATATATTAAATA
1 TTAAAATACTAAATAAATTAATTA
*
36205 TAAAAATACTAAA-AAATTCAATTA
1 TTAAAATACTAAATAAATT-AATTA
36229 TTAAAA
1 TTAAAA
36235 AATTCAATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
23 4 0.10
24 25 0.60
25 12 0.29
26 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (24 bp):
TTAAAATACTAAATAAATTAATTA
Found at i:41252 original size:18 final size:18
Alignment explanation
Indices: 41229--41263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41219 TTCCATCCGG
*
41229 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
41247 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
41264 TTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:42616 original size:45 final size:45
Alignment explanation
Indices: 42566--42655 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
42556 CAAATGCAAC
*
42566 AATTGAAAATGCATTGGACCCCACGACAATTTCAGCACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
* * * * *
42611 AATTGATAATTCATTGGCCCCCACGGCAATTGCAGGACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
42656 CACATTGGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (45 bp):
AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
Found at i:43370 original size:28 final size:28
Alignment explanation
Indices: 43330--43384 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
43320 TGCATTCGAT
43330 GAAGAAGAAGAGAGACATGGAGGAGGAG
1 GAAGAAGAAGAGAGACATGGAGGAGGAG
*
43358 GAAGAAGAAGAGAGATATGGAGGAGGA
1 GAAGAAGAAGAGAGACATGGAGGAGGA
43385 AGATGAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.05
Consensus pattern (28 bp):
GAAGAAGAAGAGAGACATGGAGGAGGAG
Found at i:46601 original size:18 final size:18
Alignment explanation
Indices: 46578--46612 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46568 TTCTATCCGG
*
46578 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
46596 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
46613 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:47965 original size:45 final size:45
Alignment explanation
Indices: 47915--48004 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
47905 CAAATGCAAC
*
47915 AATTGAAAATGCATTGGACCCCACGACAATTTCAGCACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
* * * * * *
47960 AATTGATAATTCATTGGCCCCCACGGCAATTGGAGGACCGAAAGT
1 AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
48005 CACATTGGAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (45 bp):
AATTGAAAATGCATTGGACCCCACGACAATTGCAGCACCGAAAGT
Found at i:48720 original size:28 final size:28
Alignment explanation
Indices: 48680--48734 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
48670 TGCATTCGAT
48680 GAAGAAGAAGAGAGACATGGAGGAGGAG
1 GAAGAAGAAGAGAGACATGGAGGAGGAG
*
48708 GAAGAAGAAGAGAGATATGGAGGAGGA
1 GAAGAAGAAGAGAGACATGGAGGAGGA
48735 AGATGAGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.05
Consensus pattern (28 bp):
GAAGAAGAAGAGAGACATGGAGGAGGAG
Found at i:55976 original size:17 final size:18
Alignment explanation
Indices: 55936--55976 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
55926 ATCTCCATAT
*
55936 TCTCTTCATTTTTCCTTTC
1 TCTC-TCATTTTTCCTTCC
55955 T-TCTCATTTTT-CTTCC
1 TCTCTCATTTTTCCTTCC
55971 TCTCTC
1 TCTCTC
55977 CTCTCCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
17 12 0.60
18 2 0.10
19 1 0.05
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTCATTTTTCCTTCC
Found at i:63569 original size:24 final size:26
Alignment explanation
Indices: 63542--63600 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
63532 TCCTACATGG
*
63542 TTAATTT-A-CTTCACTGTAATTTGT
1 TTAATTTCATCTTCAATGTAATTTGT
63566 TTAATTGCTTCATCTTCAATGTAATTTGT
1 TTAA-T--TTCATCTTCAATGTAATTTGT
63595 TTAATT
1 TTAATT
63601 GTTTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
24 4 0.14
25 1 0.03
26 1 0.03
27 2 0.07
28 2 0.07
29 19 0.66
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (26 bp):
TTAATTTCATCTTCAATGTAATTTGT
Found at i:63758 original size:20 final size:20
Alignment explanation
Indices: 63698--63760 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 20
63688 ACTTGTTATT
63698 TTGTTAAGGTAATCTGTTTAA
1 TTGTT-AGGTAATCTGTTTAA
** *
63719 TTGTTTATCTATAATATGTTTAA
1 TTG-TTA--GGTAATCTGTTTAA
63742 TTGTTAGGTAATCTGTTTA
1 TTGTTAGGTAATCTGTTTA
63761 GAATTTAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 10 0.30
21 4 0.12
22 5 0.15
23 14 0.42
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (20 bp):
TTGTTAGGTAATCTGTTTAA
Found at i:64975 original size:35 final size:36
Alignment explanation
Indices: 64914--64983 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
64904 ATAGGTTTTA
*
64914 TTCTTGTAAAGTGAGAAACTAAAATTAAGGACTTTG
1 TTCTTGTAAAGTAAGAAACTAAAATTAAGGACTTTG
*
64950 TTCTTGTAAA-TAAGACACTAAAATTAAGGACTTT
1 TTCTTGTAAAGTAAGAAACTAAAATTAAGGACTTT
64984 TTTATTGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 22 0.69
36 10 0.31
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (36 bp):
TTCTTGTAAAGTAAGAAACTAAAATTAAGGACTTTG
Found at i:65912 original size:16 final size:17
Alignment explanation
Indices: 65886--65919 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
65876 ATTCATTTCT
65886 ATTTACGTGAATAGTAA
1 ATTTACGTGAATAGTAA
65903 ATTT-CGTGAATAGTAA
1 ATTTACGTGAATAGTAA
65919 A
1 A
65920 AATTGTCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTAA
Found at i:68596 original size:18 final size:18
Alignment explanation
Indices: 68573--68607 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68563 TTGACTACAA
*
68573 TGAAATTCTCTCCAATCG
1 TGAAATTCTCTACAATCG
*
68591 TGAAATTGTCTACAATC
1 TGAAATTCTCTACAATC
68608 AGACTGGTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (18 bp):
TGAAATTCTCTACAATCG
Found at i:71925 original size:2 final size:2
Alignment explanation
Indices: 71918--71961 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
71908 ATATGAAGAA
71918 AT AT AT 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 AT AT AT
71960 AT
1 AT
71962 GCATATTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78589 original size:2 final size:2
Alignment explanation
Indices: 78582--78611 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
78572 AATTTATTGC
78582 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
78612 TAAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82002 original size:149 final size:142
Alignment explanation
Indices: 81744--82017 Score: 413
Period size: 149 Copynumber: 1.9 Consensus size: 142
81734 AATGAACGTG
* * *
81744 CTGATCTCATTTAGGAAGAAACTCATAATTTGTCAACTGTAAAATTATTATTAAAGAGTTCGATA
1 CTGATCTCAATTAGGAAGAAACTCATAATTTGTCAACTGTAAAATTATTATAAAAGAGTTAGATA
*
81809 AACGAACAGAATCAACAGGAGAAATTCTTCAACATACAACTCCAAGATCATAAGCAAACACTTAA
66 AACGAACAGAATCAACAGGAGAAATTCTTCAACATAAAACTCCAAGATCATAAGCAAACACTTAA
81874 TCAATAATTCTT
131 TCAATAATTCTT
*
81886 CTGATCTCAATTAGGAAGAAACTCATAATTTGTCAACAAACTGTGAAATTATTATGAATAAGAGT
1 CTGATCTCAATTAGGAAGAAACTCATAATTTGT---C-AACTGTAAAATTATTAT-AA-AAGAGT
* * *
81951 TAGATAAAACGAACAGAATCAATAGGAGAAATTCTTTAACATAAAACTCCAAGATCATGAGCAAA
60 TAGAT-AAACGAACAGAATCAACAGGAGAAATTCTTCAACATAAAACTCCAAGATCATAAGCAAA
82016 CA
124 CA
82018 GAGAAGAAGA
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
142 32 0.27
145 1 0.01
146 16 0.14
147 1 0.01
148 10 0.09
149 57 0.49
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.27
Consensus pattern (142 bp):
CTGATCTCAATTAGGAAGAAACTCATAATTTGTCAACTGTAAAATTATTATAAAAGAGTTAGATA
AACGAACAGAATCAACAGGAGAAATTCTTCAACATAAAACTCCAAGATCATAAGCAAACACTTAA
TCAATAATTCTT
Found at i:82263 original size:99 final size:96
Alignment explanation
Indices: 82041--82318 Score: 322
Period size: 99 Copynumber: 2.8 Consensus size: 96
82031 ACTCTTCAAG
* * * * *
82041 GAGAAACCATTTACTAATACCGTCTGGATCACCCACAAACCATACATTTGAAGGCCAATTGTTAA
1 GAGAAACCATTTACTAATACCTTCTGGATCACCAAC-AACCATACATTTGAAGACAAAGTGTTAA
** *
82106 AAGTTGAAACATGAAAAAAGAAGATAAACTCTAGGA
65 AACATG--ACA--AAAAAAGAAGAAAAACTCTAGGA
*
82142 GAGAAACCGTTTACTAATACCTTCTGGATCACCAACAACCATACATTTGAAGACAAAGTGTTAAA
1 GAGAAACCATTTACTAATACCTTCTGGATCACCAACAACCATACATTTGAAGACAAAGTGTTAAA
* *
82207 ACATGACAAAAGAGGAAGAAAAACTCTATACGGA
66 ACATGACAAAAAAAGAAGAAAAACTC--TA-GGA
* * * * * *
82241 GAGAACCCATTTACTAAAACCTTCTGGATCACCGACACCCATACATTTGAAGACTAAGTGTTGAA
1 GAGAAACCATTTACTAATACCTTCTGGATCACCAACAACCATACATTTGAAGACAAAGTGTTAAA
*
82306 ACATGACCAAAAA
66 ACATGACAAAAAA
82319 GCTTGCCCGC
Statistics
Matches: 154, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
96 15 0.10
98 5 0.03
99 72 0.47
100 29 0.19
101 33 0.21
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (96 bp):
GAGAAACCATTTACTAATACCTTCTGGATCACCAACAACCATACATTTGAAGACAAAGTGTTAAA
ACATGACAAAAAAAGAAGAAAAACTCTAGGA
Found at i:86308 original size:15 final size:16
Alignment explanation
Indices: 86288--86318 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
86278 AAAATACAAC
86288 ATTCTC-AGTAATCTT
1 ATTCTCTAGTAATCTT
86303 ATTCTCTAGTAATCTT
1 ATTCTCTAGTAATCTT
86319 TTATTCTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (16 bp):
ATTCTCTAGTAATCTT
Done.