Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002002.1 Hibiscus syriacus cultivar Beakdansim tig00004097_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: 111927
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:3322 original size:16 final size:17
Alignment explanation
Indices: 3301--3349 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
3291 ATCATTATTC
*
3301 TCATTATAATTATAA-A
1 TCATTATAATTAAAATA
3317 TCATTATTTAATTAAAATA
1 TCATTA--TAATTAAAATA
3336 TCATTATAAATTAA
1 TCATTAT-AATTAA
3350 TTATTTCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.21
17 1 0.04
18 14 0.50
19 7 0.25
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TCATTATAATTAAAATA
Found at i:3330 original size:18 final size:19
Alignment explanation
Indices: 3307--3342 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3297 ATTCTCATTA
*
3307 TAATTATAA-ATCATTATT
1 TAATTAAAATATCATTATT
3325 TAATTAAAATATCATTAT
1 TAATTAAAATATCATTAT
3343 AAATTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATTAAAATATCATTATT
Found at i:17932 original size:32 final size:32
Alignment explanation
Indices: 17891--18270 Score: 577
Period size: 32 Copynumber: 11.9 Consensus size: 32
17881 AGAGTCGAGA
17891 ATTACCTATGTCTTTCGGGACATATGGACAAT
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
17923 ATTACCTATGTCTTTCGGGACATATGGACAAT
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
*
17955 ATTACCTATGTCTTTTGGGACATATGGACAGA-
1 ATTACCTATGTCTTTCGGGACATATGGACA-AT
* *
17987 ATTACCTATGTTTTTCGGGACATATGGACATT
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
* *
18019 ATTACCTATGTCTTTTGGGACATATGGACAAA
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
* * *
18051 ATTACCTATATTTTTCGGGACATATGGACATT
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
*
18083 ATTACCTATGTCTTTCGGGACATATGGACAAA
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
*
18115 ATTACCTATGTCTTTCGGGACATATGGACAAA
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
*
18147 ATTACCTATGTCTTTCGGGACACATGGACAAT
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
* *
18179 ATTACATACGTCTTTCGGGACATATGGAC-AT
1 ATTACCTATGTCTTTCGGGACATATGGACAAT
**
18210 AATTACCTATGTCTTTCGACACATATGGAC-AT
1 -ATTACCTATGTCTTTCGGGACATATGGACAAT
18242 AATTACCTATGTCTTTCGGGACATATGGA
1 -ATTACCTATGTCTTTCGGGACATATGGA
18271 TAGTGACCTA
Statistics
Matches: 317, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
31 2 0.01
32 314 0.99
33 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (32 bp):
ATTACCTATGTCTTTCGGGACATATGGACAAT
Found at i:18488 original size:3 final size:3
Alignment explanation
Indices: 18480--18554 Score: 141
Period size: 3 Copynumber: 24.7 Consensus size: 3
18470 TAGGAGATGC
18480 ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18526 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18555 ATTTTATGCC
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 68 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18909 original size:21 final size:21
Alignment explanation
Indices: 18883--18947 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
18873 TGCTGAAATT
18883 ACTGTAGCAGTGTATCGGTAC
1 ACTGTAGCAGTGTATCGGTAC
18904 ACTGTAGCAGTGTATCGGTAC
1 ACTGTAGCAGTGTATCGGTAC
* *
18925 ACTGTAGCAGTGCATCGCTAC
1 ACTGTAGCAGTGTATCGGTAC
18946 AC
1 AC
18948 ATTTTAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (21 bp):
ACTGTAGCAGTGTATCGGTAC
Found at i:21142 original size:39 final size:38
Alignment explanation
Indices: 21078--21185 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 38
21068 CCTAATTCCC
* * *
21078 AAATTATTTTACCTAACATTCTAAATTCTTAATTTCTT
1 AAATTATTTCACCTAAAATTCTAAATTATTAATTTCTT
*
21116 AAATTATTTCACTGTAAAATTCTAAATTATTAATTTCTT
1 AAATTATTTCAC-CTAAAATTCTAAATTATTAATTTCTT
* *
21155 AAATTATTTTACTCTAACCATT-TAAATTATT
1 AAATTATTTCAC-CTAA-AATTCTAAATTATT
21186 TCTCAAATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 11 0.18
39 47 0.77
40 3 0.05
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (38 bp):
AAATTATTTCACCTAAAATTCTAAATTATTAATTTCTT
Found at i:21954 original size:2 final size:2
Alignment explanation
Indices: 21949--21974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21939 TAATGCACAC
21949 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
21975 TGGCATGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23193 original size:14 final size:13
Alignment explanation
Indices: 23153--23191 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
23143 TATTGAAAGC
23153 TAAATA-TTAAAA
1 TAAATATTTAAAA
*
23165 TAATTCATTTAAAA
1 TAAAT-ATTTAAAA
23179 TAAATATTTAAAA
1 TAAATATTTAAAA
23192 ATTTAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 9 0.39
14 10 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTTAAAA
Found at i:23889 original size:13 final size:13
Alignment explanation
Indices: 23871--23899 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23861 CCACCGTACT
23871 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
23884 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
23897 CCG
1 CCG
23900 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:24610 original size:11 final size:11
Alignment explanation
Indices: 24594--24648 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
24584 TTTGGGTTTG
* *
24594 TAATAATTATT
1 TAATAATAATA
24605 TAATAATAATA
1 TAATAATAATA
24616 TAATAATAATA
1 TAATAATAATA
*
24627 T-ATAATATTTA
1 TAATAATA-ATA
24638 TAATAATAATA
1 TAATAATAATA
24649 ATTTTAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 6 0.16
11 26 0.68
12 6 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATAATAATA
Found at i:24611 original size:3 final size:3
Alignment explanation
Indices: 24605--24669 Score: 60
Period size: 3 Copynumber: 21.7 Consensus size: 3
24595 AATAATTATT
* *
24605 TAA TAA TAA T-A TAA TAA TAA TATA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
** **
24650 TTT TAA TTT TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
24670 TTTAAGTAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (3 bp):
TAA
Found at i:24668 original size:36 final size:36
Alignment explanation
Indices: 24605--24673 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
24595 AATAATTATT
24605 TAATAATAATATAATAATAATATATAATATTTATAA
1 TAATAATAATATAATAATAATATATAATATTTATAA
* **
24641 TAATAATAATTTTAATTTTAATA-ATAATATTTA
1 TAATAATAA-TATAATAATAATATATAATATTTA
24674 AGTAAAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (36 bp):
TAATAATAATATAATAATAATATATAATATTTATAA
Found at i:24926 original size:76 final size:76
Alignment explanation
Indices: 24824--25924 Score: 1934
Period size: 76 Copynumber: 14.4 Consensus size: 76
24814 GAGGTCTTAA
* * * *
24824 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
24889 AGGCTTTTTGG
66 AGGCTTTTTGG
24900 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
24965 AGGCTTTTTGG
66 AGGCTTTTTGG
*
24976 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25041 AGGCTTTTTGG
66 AGGCTTTTTGG
25052 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25117 AGGCTTTTTGG
66 AGGCTTTTTGG
*
25128 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25193 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
25204 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25269 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
25280 AAACATTATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25344 AGGCTTTTTGG
66 AGGCTTTTTGG
25355 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25420 AGGCTTTTTTTGG
66 AGGC--TTTTTGG
*
25433 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25498 AGGCTTTTTTTGG
66 AGGC--TTTTTGG
* * *
25511 AAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25576 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
25587 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25652 AGGCTTTTTGG
66 AGGCTTTTTGG
*
25663 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25728 AGGCTTTTTGG
66 AGGCTTTTTGG
25739 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25804 AGGCTTTTTTTGG
66 AGGC--TTTTTGG
* *
25817 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
25882 AGGCTTTTTTTGG
66 AGGC--TTTTTGG
*
25895 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
25925 TGAGAAATAG
Statistics
Matches: 993, Mismatches: 27, Indels: 8
0.97 0.03 0.01
Matches are distributed among these distances:
75 71 0.07
76 659 0.66
78 263 0.26
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
AGGCTTTTTGG
Found at i:29521 original size:83 final size:83
Alignment explanation
Indices: 29382--29636 Score: 483
Period size: 83 Copynumber: 3.1 Consensus size: 83
29372 CTTATTTCTC
* * *
29382 CTATGAGCAAATTCATCTTTTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
29447 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
29465 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
29530 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
29548 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
29613 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
29631 CTATGA
1 CTATGA
29637 TCCCAATTAC
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 169 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:31943 original size:13 final size:13
Alignment explanation
Indices: 31921--31955 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
31911 CTTGATTCAA
*
31921 TTTTCCTTTTTCT
1 TTTTCTTTTTTCT
31934 TTTTCTTTTTTCT
1 TTTTCTTTTTTCT
31947 TCTTTCTTT
1 T-TTTCTTT
31956 GTTAGATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTTTCT
Found at i:37340 original size:14 final size:13
Alignment explanation
Indices: 37300--37338 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
37290 TATTGAAAGC
37300 TAAATA-TTAAAA
1 TAAATATTTAAAA
*
37312 TAATTCATTTAAAA
1 TAAAT-ATTTAAAA
37326 TAAATATTTAAAA
1 TAAATATTTAAAA
37339 ATTTAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 9 0.39
14 10 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATTTAAAA
Found at i:37459 original size:18 final size:19
Alignment explanation
Indices: 37436--37473 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
37426 ATATATTTTA
37436 AAAACA-ATAAAATAAATG
1 AAAACATATAAAATAAATG
37454 AAAACATATAAAATAAATG
1 AAAACATATAAAATAAATG
37473 A
1 A
37474 CTAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAACATATAAAATAAATG
Found at i:38045 original size:13 final size:13
Alignment explanation
Indices: 38027--38055 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38017 CCACCGTACT
38027 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
38040 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
38053 CCG
1 CCG
38056 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:38768 original size:3 final size:3
Alignment explanation
Indices: 38762--38835 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
38752 AATAATTATT
* *
38762 TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** **
38808 TAA TAA TTT TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
38836 TTAAGTAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:38770 original size:14 final size:14
Alignment explanation
Indices: 38751--38808 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
38741 TTTGGGTTTG
38751 TAATAATTATTTAA
1 TAATAATTATTTAA
38765 TAATAA-TA--TAA
1 TAATAATTATTTAA
* *
38776 TAATAATAATATAA
1 TAATAATTATTTAA
38790 TAATAA-TATTT-A
1 TAATAATTATTTAA
38802 TAATAAT
1 TAATAAT
38809 AATAATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 9 0.24
12 8 0.22
13 5 0.14
14 15 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATAATTATTTAA
Found at i:43215 original size:13 final size:13
Alignment explanation
Indices: 43197--43221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43187 GTCTTAAATT
43197 TTAATTTTTTATG
1 TTAATTTTTTATG
43210 TTAATTTTTTAT
1 TTAATTTTTTAT
43222 TTTATTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTAATTTTTTATG
Found at i:52766 original size:24 final size:24
Alignment explanation
Indices: 52739--52826 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
52729 TTCTATTATA
*
52739 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
52763 ATACTTGACCTGGATTCTGATTGA
1 ATACTTGACCTGGATTCTGATCGG
* * *
52787 ATACTTGACATGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
52811 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
52827 ATTTTATGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:58345 original size:3 final size:3
Alignment explanation
Indices: 58337--58368 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
58327 TAAATTTCAA
58337 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58369 ATTAAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:58582 original size:2 final size:2
Alignment explanation
Indices: 58577--58615 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
58567 ATATTGAAGA
*
58577 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58616 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65816 original size:23 final size:23
Alignment explanation
Indices: 65790--65862 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
65780 ATATTTTACA
*
65790 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
65813 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
65836 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
65859 ATAT
1 ATAT
65863 TTTTACCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:66316 original size:23 final size:23
Alignment explanation
Indices: 66281--66353 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
66271 ATACTTTACA
*
66281 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
66304 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
66327 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
66350 ATAT
1 ATAT
66354 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:66379 original size:491 final size:488
Alignment explanation
Indices: 65388--67727 Score: 3942
Period size: 476 Copynumber: 4.8 Consensus size: 488
65378 TTATAATATG
*
65388 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAATTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
65453 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
65518 C-AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
*
65582 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* * ** ** *
65647 ACCGTAACATAACAAATAAATCATTAGATACAAATAATTACTAAATTGATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
65712 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
325 CAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
* *
65777 TAGATATTTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
389 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
65842 GCGCTACCTATTACATCATATTTTTACCTATTATA
454 GCGCTACCTATTACATCATATTTTTACCTATTATA
* * *
65877 TTGAAAGTGTCCATACTTTTTATAAAAATGATAGATATTTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA-CTTTTTTTAAAGTTATGTAATTTATGT
* *
65942 TTCAATTTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
65 TTTAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC
*
66007 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGCATTTAAATTTAACAATA
129 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATA
**
66072 TTAATTAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
194 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
66137 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
259 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
66202 TCAAAATATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACATTTTTATAAAAATG
324 TCAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATG
66267 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
388 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
66332 AGTGCTACCTATTACATCATATTTTTACCTATTATA
453 AGCGCTACCTATTACATCATATTTTTACCTATTATA
* *
66368 TTGAAAGTGTCCATACTTTTTATAAAAAGGATTGATACTTTTTATAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
66433 TTAATTTTTTTAATAGTGTTTCATGTTTTCAACCTACAATATTAATTTAATAATTTCATTTACAC
66 TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66498 -AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
66562 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* * * *
66627 CCGTAACATAAAAAATAAATCATTAGACACTTATAATAACTAAATTAATATCTT-AAA---A--C
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
* * *
66686 -----TAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACACATTTATAAAAAGGATA
326 AAAAATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATA
*
66746 TATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
391 GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
66811 GCTACCTATTACATCATATTTTTACCTATTATA
456 GCTACCTATTACATCATATTTTTACCTATTATA
* *
66844 TTGAAAGTGTCCATACTTTTTATAAAAAATGATCGACACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTAT-AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* * *
66909 TTCAA-TTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTTATTTACA
65 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66973 CAAAAAATTATTTGATTGTTTTGATATTTTA-AAAATATTATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
*
67037 TAACCAAAGATAATAATAAATATTTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
67102 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTT-AAA---A--
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
67161 C-----TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGAT
325 CAAAAATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGAT
67221 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
390 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
* * *
67286 GGCTATCTATTACATTATATTTTTACCTATTATA
455 CGCTACCTATTACATCATATTTTTACCTATTATA
*
67320 TTGAAAGTGTCCATATTTTTTATAAAAAGGATCGATA-TTTTTTTAAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTT-AAAGTTATGTAATTTATGT
* *
67384 TTTAATTTTTTTAATAGTCTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTACA
65 TTTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
67449 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
*
67514 TAACCAAAAATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
67579 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
67644 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
325 CAAAA-ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGA
*
67709 TAGATATTTTACAATATAA
389 TAGATACTTTACAATATAA
67728 CAGATAAAAA
Statistics
Matches: 1754, Mismatches: 77, Indels: 40
0.94 0.04 0.02
Matches are distributed among these distances:
474 7 0.00
475 35 0.02
476 645 0.37
477 219 0.12
478 3 0.00
481 1 0.00
482 1 0.00
483 1 0.00
484 1 0.00
487 3 0.00
488 195 0.11
489 179 0.10
490 88 0.05
491 376 0.21
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (488 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATA
GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
GCTACCTATTACATCATATTTTTACCTATTATA
Found at i:66792 original size:23 final size:23
Alignment explanation
Indices: 66757--66829 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
66747 ATACTTTACA
*
66757 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
66780 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
66803 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
66826 ATAT
1 ATAT
66830 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:67268 original size:23 final size:23
Alignment explanation
Indices: 67233--67305 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
67223 ATACTTTACA
*
67233 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
67256 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
67279 ATATAAGGGCTATCTATTACATT
1 ATATAAGCGCTACCTATTACATT
67302 ATAT
1 ATAT
67306 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:70844 original size:30 final size:30
Alignment explanation
Indices: 70808--70864 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
70798 AACACCTTAA
** *
70808 AAAAATAAATAAGTGAATATAAATACATTC
1 AAAAATAAATAAACGAATACAAATACATTC
70838 AAAAATAAATAAACGAATACAAATACA
1 AAAAATAAATAAACGAATACAAATACA
70865 ACACTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (30 bp):
AAAAATAAATAAACGAATACAAATACATTC
Found at i:71782 original size:15 final size:15
Alignment explanation
Indices: 71762--71792 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71752 CAACAAATAG
71762 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
71777 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
71792 A
1 A
71793 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:73494 original size:24 final size:24
Alignment explanation
Indices: 73464--73572 Score: 121
Period size: 24 Copynumber: 4.6 Consensus size: 24
73454 TGTTAATTTA
*
73464 TTGTGTTCGTTTACGTTCGTTCAT
1 TTGTGTTCGTTTATGTTCGTTCAT
* * *
73488 TTGTGTTTGTTTATGTTCTTTTA-
1 TTGTGTTCGTTTATGTTCGTTCAT
* * *
73511 TTGTGTTCGTTTATGTTAGTTTAC
1 TTGTGTTCGTTTATGTTCGTTCAT
* **
73535 ATCCGTTCGTTTATGTTCGTTCAT
1 TTGTGTTCGTTTATGTTCGTTCAT
73559 TTGTGTTCGTTTAT
1 TTGTGTTCGTTTAT
73573 CATTTAAATG
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.29
24 48 0.71
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.59
Consensus pattern (24 bp):
TTGTGTTCGTTTATGTTCGTTCAT
Found at i:73547 original size:47 final size:47
Alignment explanation
Indices: 73460--73572 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
73450 TTTGTGTTAA
* * ** ** * *
73460 TTTATTGTGTTCGTTTACGTTCGTTCATTTGTGTTTGTTTATGTTCT
1 TTTATTGTGTTCGTTTATGTTAGTTCACATCCGTTCGTTTATGTTCG
*
73507 TTTATTGTGTTCGTTTATGTTAGTTTACATCCGTTCGTTTATGTTCG
1 TTTATTGTGTTCGTTTATGTTAGTTCACATCCGTTCGTTTATGTTCG
*
73554 TTCATTTGTGTTCGTTTAT
1 TTTA-TTGTGTTCGTTTAT
73573 CATTTAAATG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 41 0.75
48 14 0.25
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.59
Consensus pattern (47 bp):
TTTATTGTGTTCGTTTATGTTAGTTCACATCCGTTCGTTTATGTTCG
Found at i:73957 original size:19 final size:21
Alignment explanation
Indices: 73919--73957 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
73909 AATTTTAAAA
*
73919 TAAATATAAACTAGTATAATT
1 TAAATATAAACTAATATAATT
73940 TAAAT-TAAA-TAATATAAT
1 TAAATATAAACTAATATAAT
73958 CTATTTAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATATAAACTAATATAATT
Found at i:77846 original size:24 final size:24
Alignment explanation
Indices: 77818--77881 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
77808 CATCGATGCA
*
77818 TAAGGAGTGCATCGATGCACACGT
1 TAAGGAGTGCATCGATGCACACGG
77842 TAAGG-GATGCATCGAT--ACACGG
1 TAAGGAG-TGCATCGATGCACACGG
77864 T-AGGA-TGCATCGATGCAC
1 TAAGGAGTGCATCGATGCAC
77882 TTCAAGGGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 9 0.26
21 3 0.09
22 8 0.23
23 1 0.03
24 14 0.40
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (24 bp):
TAAGGAGTGCATCGATGCACACGG
Found at i:86440 original size:19 final size:21
Alignment explanation
Indices: 86402--86440 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
86392 AATTTTAAAA
*
86402 TAAATATAAACTAGTATAATT
1 TAAATATAAACTAATATAATT
86423 TAAAT-TAAA-TAATATAAT
1 TAAATATAAACTAATATAAT
86441 CTATTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TAAATATAAACTAATATAATT
Found at i:91234 original size:29 final size:29
Alignment explanation
Indices: 91192--91273 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
91182 AAACTAAATT
*
91192 GATGTCATTGCTTACATTATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
91221 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
91250 GATGACATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
91274 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:95978 original size:29 final size:29
Alignment explanation
Indices: 95936--96017 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
95926 AAACTAAATT
95936 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
95965 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
95994 GATATCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
96018 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:98107 original size:6 final size:6
Alignment explanation
Indices: 98096--98123 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
98086 AAATATCTCT
98096 TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTAT
98124 TATGTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTATAA
Found at i:104140 original size:11 final size:10
Alignment explanation
Indices: 104067--104146 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
104057 TTCGATAATA
104067 TAATAATTATT
1 TAATAA-TATT
* *
104078 TTATAGTATT
1 TAATAATATT
104088 TAGATAA-ATT
1 TA-ATAATATT
104098 TAATAATAATT
1 TAATAAT-ATT
* *
104109 TTATAATCTTT
1 TAATAAT-ATT
104120 TAATAA-ATT
1 TAATAATATT
104129 TAATAAGTATT
1 TAATAA-TATT
*
104140 TTATAAT
1 TAATAAT
104147 TTTTTAAACT
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
9 12 0.22
10 11 0.20
11 31 0.57
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (10 bp):
TAATAATATT
Found at i:104152 original size:31 final size:30
Alignment explanation
Indices: 104067--104153 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
104057 TTCGATAATA
* *
104067 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
*
104098 TAATAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
104129 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
104154 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.86
32 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:104249 original size:24 final size:24
Alignment explanation
Indices: 104213--104266 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 24
104203 ATACTTTATT
104213 TAAAAAAAATAT-ATTAAACTTAG
1 TAAAAAAAATATAATTAAACTTAG
*
104236 TAAAAAATAGTATACAATTAAACTTAG
1 TAAAAAA-A--ATATAATTAAACTTAG
104263 TAAA
1 TAAA
104267 CTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 1 0.04
26 3 0.12
27 15 0.58
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (24 bp):
TAAAAAAAATATAATTAAACTTAG
Found at i:104894 original size:31 final size:30
Alignment explanation
Indices: 104859--104945 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
104849 TCAATAAAGT
104859 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* **
104890 TTAAAAGATTATAAAATTATTAACAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
104921 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
104946 TATTATCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 42 0.91
32 3 0.07
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:107631 original size:39 final size:39
Alignment explanation
Indices: 107521--107642 Score: 162
Period size: 38 Copynumber: 3.2 Consensus size: 39
107511 ACCATTTCAT
* * * * *
107521 TAAACATTTTAT-ATTTTCAATTTTGTAAAAAAAATATA
1 TAAATATTTTATGAATTTAAATTTTTTAAAGAAAATATA
*
107559 T-AA-ATTTTATGAATTTAATTTTTTTAAAG-AAATATA
1 TAAATATTTTATGAATTTAAATTTTTTAAAGAAAATATA
107595 TAAATATTTTATGAATTTAAATTTTTTAAAGAAAATATA
1 TAAATATTTTATGAATTTAAATTTTTTAAAGAAAATATA
107634 TAAATATTT
1 TAAATATTT
107643 CCAACTTCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
36 15 0.20
37 17 0.23
38 26 0.35
39 16 0.22
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.48
Consensus pattern (39 bp):
TAAATATTTTATGAATTTAAATTTTTTAAAGAAAATATA
Found at i:109411 original size:29 final size:29
Alignment explanation
Indices: 109378--109451 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
109368 TTGATGTCAT
*
109378 TGCTTACATCATTTAATTAAAGATATCAA
1 TGCTTACATCATTTAAGTAAAGATATCAA
* * *
109407 TGCTTACATCATTTAAGTAATGATGTCAT
1 TGCTTACATCATTTAAGTAAAGATATCAA
109436 TGCTTACATCAATTTA
1 TGCTTACATC-ATTTA
109452 GTTAGGTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 35 0.88
30 5 0.12
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (29 bp):
TGCTTACATCATTTAAGTAAAGATATCAA
Found at i:111510 original size:6 final size:6
Alignment explanation
Indices: 111499--111532 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
111489 AAATATCTCT
111499 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTAT
111533 TATGTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTATAA
Done.