Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013803.1 Kokia drynarioides strain JFW-HI SEQ_128831, 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: 164226
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:20145 original size:31 final size:32
Alignment explanation
Indices: 20085--20146 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
20075 CAATTCTTCA
* *
20085 TTTTCCCCCTTTTATGTATTTTTTATTTTTGG
1 TTTTCCCCCTTTTATCTATTCTTTATTTTTGG
* *
20117 TTTTCCCCTTTTTATCT-TTCTTTGTTTTTG
1 TTTTCCCCCTTTTATCTATTCTTTATTTTTG
20147 ATTATCCAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.06, C:0.18, G:0.08, T:0.68
Consensus pattern (32 bp):
TTTTCCCCCTTTTATCTATTCTTTATTTTTGG
Found at i:32262 original size:20 final size:21
Alignment explanation
Indices: 32223--32264 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
32213 ATATTATAAA
*
32223 AATAAAATTAATTTATTTAAT
1 AATAAAATTAATTAATTTAAT
*
32244 AATAAAA-TGATTAATTTAAT
1 AATAAAATTAATTAATTTAAT
32264 A
1 A
32265 CAATCTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
AATAAAATTAATTAATTTAAT
Found at i:40939 original size:15 final size:15
Alignment explanation
Indices: 40892--40945 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
40882 AAGTATGTTT
40892 ATTAAAATTGATCAA
1 ATTAAAATTGATCAA
* * *
40907 ATCGAAAAAT-ATAAAA
1 AT-TAAAATTGAT-CAA
40923 ATTAAAATTGATCAA
1 ATTAAAATTGATCAA
40938 ATTAAAAT
1 ATTAAAAT
40946 ATAATTATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (15 bp):
ATTAAAATTGATCAA
Found at i:40955 original size:29 final size:30
Alignment explanation
Indices: 40890--40957 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
40880 AAAAGTATGT
40890 TTATTAAAATTGATCAAATCGAAAAATATAA
1 TTATTAAAATTGATCAAATC-AAAAATATAA
** *
40921 AAATTAAAATTGATCAAAT-TAAAATATAA
1 TTATTAAAATTGATCAAATCAAAAATATAA
40950 TTATTAAA
1 TTATTAAA
40958 TATTCAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
31 17 0.53
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (30 bp):
TTATTAAAATTGATCAAATCAAAAATATAA
Found at i:43633 original size:58 final size:58
Alignment explanation
Indices: 43506--43637 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
43496 GTTCGAGGTT
* * * **
43506 AAAAATGAAATTTTTAGACACCCGAGGGTAAAACGGTAACTTTAAAAAAATCGGGATC
1 AAAAATGGAATTTTTGGACACCCGAGGGTAAAACGATAACTTTAAAAAAATCGAAATC
** * * * **
43564 AAAAACAGAATTTTTGGACATCCGAGGGTAAAATGATAATTTTTAGGAAAATCGAAATC
1 AAAAATGGAATTTTTGGACACCCGAGGGTAAAACGATAA-CTTTAAAAAAATCGAAATC
43623 -AAAATGGAATTTTTG
1 AAAAATGGAATTTTTG
43638 TAATTAAATA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
58 45 0.76
59 14 0.24
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.27
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGACACCCGAGGGTAAAACGATAACTTTAAAAAAATCGAAATC
Found at i:44067 original size:21 final size:22
Alignment explanation
Indices: 44023--44068 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
44013 AAGCTTCTTT
**
44023 TTTTTTTTCATTTTCTCTTTTTC
1 TTTTTTTTCA-TTTCTCTCCTTC
44046 TTTTTTTTCA-TTCTCTCCTTC
1 TTTTTTTTCATTTCTCTCCTTC
44067 TT
1 TT
44069 CATCCTTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
23 10 0.48
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTTTTTCATTTCTCTCCTTC
Found at i:44561 original size:3 final size:3
Alignment explanation
Indices: 44555--44603 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
44545 TTAAAAAAAG
* * *
44555 TTA TTA TTG TCA TTA TTA ATA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
44601 TTA
1 TTA
44604 ACCATTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:45322 original size:6 final size:6
Alignment explanation
Indices: 45311--45376 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
45301 TCAAATTTGA
** * *
45311 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAAAAG ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT--AAAT TTAAAT TTAAAT
* *
45360 TTAAAA ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
45377 CCAATTTAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
5 3 0.07
6 38 0.84
8 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:45785 original size:21 final size:22
Alignment explanation
Indices: 45754--45804 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
45744 TCATGGTTGA
*
45754 CTTTTTT-TCTAGTCCTTTC-T
1 CTTTTTTATCTAGTCATTTCAT
45774 CTTTTTTATCTAGTCATTTCAT
1 CTTTTTTATCTAGTCATTTCAT
*
45796 ATTTTTTAT
1 CTTTTTTAT
45805 TTTTACACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 7 0.26
21 11 0.41
22 9 0.33
ACGTcount: A:0.14, C:0.18, G:0.04, T:0.65
Consensus pattern (22 bp):
CTTTTTTATCTAGTCATTTCAT
Found at i:46056 original size:14 final size:16
Alignment explanation
Indices: 46037--46070 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
46027 TAAGTAAAAA
46037 ATAATATA-AA-CTTT
1 ATAATATATAATCTTT
46051 ATAATATATAATCTTT
1 ATAATATATAATCTTT
46067 ATAA
1 ATAA
46071 CTAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATATATAATCTTT
Found at i:46061 original size:16 final size:16
Alignment explanation
Indices: 46040--46070 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46030 GTAAAAAATA
46040 ATATAAACTTTATAAT
1 ATATAAACTTTATAAT
*
46056 ATATAATCTTTATAA
1 ATATAAACTTTATAA
46071 CTAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAAACTTTATAAT
Found at i:53244 original size:3 final size:3
Alignment explanation
Indices: 53236--53261 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53226 AGGATGCGGC
53236 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
53262 AATATGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:56206 original size:39 final size:40
Alignment explanation
Indices: 56155--56236 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 40
56145 AAAAATTATA
56155 TTTAATACAATAAAATATTTATTACATTTATAGTATT-TT
1 TTTAATACAATAAAATATTTATTACATTTATAGTATTGTT
* * *
56194 TTTAATATAATAAAATATTTATTATATTTATGGTATTGTT
1 TTTAATACAATAAAATATTTATTACATTTATAGTATTGTT
56234 TTT
1 TTT
56237 TTAGTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 34 0.87
40 5 0.13
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (40 bp):
TTTAATACAATAAAATATTTATTACATTTATAGTATTGTT
Found at i:56736 original size:26 final size:26
Alignment explanation
Indices: 56707--56757 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
56697 TTATTTTTAA
*
56707 TTTAGTGTA-TAATAATTTTATATATT
1 TTTAATGTATTAA-AATTTTATATATT
*
56733 TTTAATTTATTAAAATTTTATATAT
1 TTTAATGTATTAAAATTTTATATAT
56758 AACTATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTAATGTATTAAAATTTTATATATT
Found at i:59195 original size:7 final size:7
Alignment explanation
Indices: 59183--59216 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
59173 TAAAAGGTAG
59183 AATTAAA
1 AATTAAA
59190 AATTAAA
1 AATTAAA
59197 AATTAAA
1 AATTAAA
59204 AATTAAA
1 AATTAAA
59211 AATTAA
1 AATTAA
59217 TTGAACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATTAAA
Found at i:61815 original size:3 final size:3
Alignment explanation
Indices: 61809--61850 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
61799 AACTTTATTA
*
61809 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
61851 GAGCTCAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:61916 original size:17 final size:17
Alignment explanation
Indices: 61896--61998 Score: 136
Period size: 17 Copynumber: 6.1 Consensus size: 17
61886 ATTGAACCTA
61896 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
61913 ATTTTACATTTAAATTT
1 ATTTTAAATTTAAATTT
*
61930 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
61947 ATCTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
61964 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
* *
61981 ACTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
61998 A
1 A
61999 AAATTTAATT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
16 6 0.08
17 69 0.92
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:61929 original size:6 final size:6
Alignment explanation
Indices: 61898--62019 Score: 71
Period size: 6 Copynumber: 21.0 Consensus size: 6
61888 TGAACCTAAT
* * *
61898 TTTAAA TTTTAAA -TT-AT TTTACA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
61944 CTT--A TCTTGAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AC TTTGAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
61989 TTTAAA TTTAAAA TTT-AA TTAAAA GTTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA -TTTAAA
62020 AATTACAAGT
Statistics
Matches: 88, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.02
5 22 0.25
6 45 0.51
7 19 0.22
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:61937 original size:11 final size:11
Alignment explanation
Indices: 61915--61999 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
61905 TTTAAATTAT
61915 TTTACATTTAAA
1 TTTA-ATTTAAA
*
61927 TTTATTTTAAA
1 TTTAATTTAAA
* **
61938 TTTAAACTTATC
1 TTT-AATTTAAA
*
61950 TTGAATTTAAA
1 TTTAATTTAAA
*
61961 TTTATTTTAAA
1 TTTAATTTAAA
*
61972 TTTAAATTT-AC
1 TTT-AATTTAAA
61983 TTTGAATTTAAA
1 TTT-AATTTAAA
61995 TTTAA
1 TTTAA
62000 AATTTAATTA
Statistics
Matches: 55, Mismatches: 15, Indels: 7
0.71 0.19 0.09
Matches are distributed among these distances:
11 37 0.67
12 18 0.33
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:61939 original size:51 final size:51
Alignment explanation
Indices: 61884--61990 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
61874 CATTTAAACC
* * * *
61884 AAATTGAACCTAATTTTAAATTTTAAA-TTATTTTACATTTAAATTTATTTT
1 AAATTGAAACTAATCTTAAA-TTTAAATTTATTTTAAATTTAAATTTACTTT
* * *
61935 AAATTTAAACTTATCTTGAATTTAAATTTATTTTAAATTTAAATTTACTTT
1 AAATTGAAACTAATCTTAAATTTAAATTTATTTTAAATTTAAATTTACTTT
*
61986 GAATT
1 AAATT
61991 TAAATTTAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 6 0.13
51 41 0.87
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (51 bp):
AAATTGAAACTAATCTTAAATTTAAATTTATTTTAAATTTAAATTTACTTT
Found at i:63758 original size:30 final size:31
Alignment explanation
Indices: 63722--64022 Score: 132
Period size: 30 Copynumber: 10.2 Consensus size: 31
63712 AAAAAGTCCT
*
63722 TAAAC-TTTCCAAAAATCATAC-TTTATCCCC
1 TAAACTTTTCCAAAAATCATACTTTTA-ACCC
63752 TAAACTTTTCC-AAAAT--TACTTTTAACCC
1 TAAACTTTTCCAAAAATCATACTTTTAACCC
*
63780 TCAAACTTTTCCAAAAATCATA-TTTTGA-CC
1 T-AAACTTTTCCAAAAATCATACTTTTAACCC
* * * * * *
63810 TCAAACTTTTCC-AAAATTAAAATATGACCCC
1 T-AAACTTTTCCAAAAATCATACTTTTAACCC
* *
63841 TAAACTTTTCC--AAATTATA-TTTTGACCC
1 TAAACTTTTCCAAAAATCATACTTTTAACCC
*
63869 TTAAACTTTTCC-AAAAT-A-ACATTTTTACCC
1 -TAAACTTTTCCAAAAATCATAC-TTTTAACCC
* *
63899 TTAAACTTCT-C-AAAAT--TACATTTTGACCCC
1 -TAAACTTTTCCAAAAATCATAC-TTTT-AACCC
* *
63929 TAAACTTTT-CTAAAAT--TACATTTTAACTCT
1 TAAACTTTTCCAAAAATCATAC-TTTTAAC-CC
* * *
63959 TAAACTTTTCC-AAAATCACA-TTTTTATCC
1 TAAACTTTTCCAAAAATCATACTTTTAACCC
* * *
63988 TGAAC--TTCCAAAAATCACAATTTT-ACCC
1 TAAACTTTTCCAAAAATCATACTTTTAACCC
64016 TCAAACT
1 T-AAACT
64023 AAAAAAATCA
Statistics
Matches: 221, Mismatches: 27, Indels: 46
0.75 0.09 0.16
Matches are distributed among these distances:
27 4 0.02
28 26 0.12
29 76 0.34
30 98 0.44
31 14 0.06
32 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (31 bp):
TAAACTTTTCCAAAAATCATACTTTTAACCC
Found at i:63786 original size:29 final size:29
Alignment explanation
Indices: 63749--63974 Score: 187
Period size: 30 Copynumber: 7.7 Consensus size: 29
63739 ATACTTTATC
*
63749 CCCT-AAACTTTTCCAAAATTACTTTTAA
1 CCCTCAAACTTTTCCAAAATTACTTTTGA
63777 CCCTCAAACTTTTCCAAAAATCATA-TTTTGA
1 CCCTCAAACTTTTCC-AAAAT--TACTTTTGA
** *
63808 -CCTCAAACTTTTCCAAAATTAAAATATGA
1 CCCTCAAACTTTTCCAAAATT-ACTTTTGA
*
63837 CCC-CTAAACTTTTCC-AAATTATATTTTGA
1 CCCTC-AAACTTTTCCAAAATTA-CTTTTGA
* * *
63866 CCCTTAAACTTTTCCAAAATAACATTTTTA
1 CCCTCAAACTTTTCCAAAATTAC-TTTTGA
* *
63896 CCCTTAAACTTCT-CAAAATTACATTTTGA
1 CCCTCAAACTTTTCCAAAATTAC-TTTTGA
* *
63925 CCC-CTAAACTTTTCTAAAATTACATTTTAA
1 CCCTC-AAACTTTTCCAAAATTAC-TTTTGA
* *
63955 CTCTTAAACTTTTCCAAAAT
1 CCCTCAAACTTTTCCAAAAT
63975 CACATTTTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.01
28 6 0.04
29 67 0.41
30 83 0.51
31 5 0.03
32 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTCAAACTTTTCCAAAATTACTTTTGA
Found at i:63983 original size:89 final size:87
Alignment explanation
Indices: 63748--64000 Score: 305
Period size: 89 Copynumber: 2.9 Consensus size: 87
63738 CATACTTTAT
* * * *
63748 CCCCTAAACTTTTCCAAAATTAC-TTTTAACCCTCAAACTTTTCCAAAAATCATATTTTGACCTC
1 CCCCTAAACTTTT-CAAAATTACATTTTAACCCTTAAACTTTTCC-AAAATCACATTTTTACCTT
*
63812 AAACTTTTCCAAAATTAAAATATGA
64 AAACTTCT-CAAAATTAAAATATGA
* * * *
63837 CCCCTAAACTTTTCCAAATTATATTTTGACCCTTAAACTTTTCCAAAATAACATTTTTACCCTTA
1 CCCCTAAACTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTTA-CCTTA
* * *
63902 AACTTCTCAAAATTACATTTTGA
65 AACTTCTCAAAATTAAAATATGA
*
63925 CCCCTAAACTTTTCTAAAATTACATTTTAACTCTTAAACTTTTCCAAAATCACATTTTTATCC-T
1 CCCCTAAACTTTTC-AAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTTA-CCTT
*
63989 GAACTTC-CAAAA
64 AAACTTCTCAAAA
64001 ATCACAATTT
Statistics
Matches: 142, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
87 5 0.04
88 53 0.37
89 84 0.59
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (87 bp):
CCCCTAAACTTTTCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATCACATTTTTACCTTAA
ACTTCTCAAAATTAAAATATGA
Found at i:63994 original size:59 final size:59
Alignment explanation
Indices: 63719--63982 Score: 279
Period size: 59 Copynumber: 4.5 Consensus size: 59
63709 CCCAAAAAGT
*
63719 CCTTAAAC-TTTCCAAAAATCATACTTTAT-CCCCTAAACTTTTCCAAAATTAC-TTTTAAC
1 CCTTAAACTTTTCC-AAAATCATA-TTT-TGACCCTAAACTTTTCCAAAATTACATTTTAAC
* * * * *
63778 CCTCAAACTTTTCCAAAAATCATATTTTGA-CCTCAAACTTTTCCAAAATTAAAATATGAC
1 CCTTAAACTTTTCC-AAAATCATATTTTGACCCT-AAACTTTTCCAAAATTACATTTTAAC
* * * *
63838 CCCTAAACTTTTCC-AAATTATATTTTGACCCTTAAACTTTTCCAAAATAACATTTTTAC
1 CCTTAAACTTTTCCAAAATCATATTTTGACCC-TAAACTTTTCCAAAATTACATTTTAAC
* * * *
63897 CCTTAAACTTCT-CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCTTAAACTTTTCCAAAATCATATTTTGA-CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
63956 TCTTAAACTTTTCCAAAATCACATTTT
1 CCTTAAACTTTTCCAAAATCATATTTT
63983 TATCCTGAAC
Statistics
Matches: 173, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
58 18 0.10
59 107 0.62
60 48 0.28
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (59 bp):
CCTTAAACTTTTCCAAAATCATATTTTGACCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:64108 original size:57 final size:55
Alignment explanation
Indices: 63966--64126 Score: 157
Period size: 57 Copynumber: 2.8 Consensus size: 55
63956 TCTTAAACTT
63966 TTCCAAAATCACATTTTTA-TCCTGAACTTCCAAAAATCACAATTTTACCCTCAAAC
1 TTCCAAAATCACATTTTTACT-CTGAACTTCCAAAAA-CACAATTTTACCCTCAAAC
*** * * *
64022 TAAAAAAATCACATTTTTACCCCCGAACTTCCAAAAA-ACATATTTATACCCTCGAAC
1 TTCCAAAATCACATTTTTA-CTCTGAACTTCCAAAAACACA-ATTT-TACCCTCAAAC
* *
64079 TTCCTAAAATCACATTTTGACTCTAAACTTTCCAAAAATCAC-ATTTTA
1 TTCC-AAAATCACATTTTTACTCTGAAC-TTCCAAAAA-CACAATTTTA
64127 ACCTTAAATT
Statistics
Matches: 84, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
55 3 0.04
56 20 0.24
57 32 0.38
58 27 0.32
60 2 0.02
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (55 bp):
TTCCAAAATCACATTTTTACTCTGAACTTCCAAAAACACAATTTTACCCTCAAAC
Found at i:64134 original size:29 final size:29
Alignment explanation
Indices: 63719--64134 Score: 216
Period size: 29 Copynumber: 14.2 Consensus size: 29
63709 CCCAAAAAGT
* *
63719 CCTTAAACTTTCCAAAAATCATACTTTATC
1 CCTTAAACTTTCCAAAAATCACATTTTA-C
* *
63749 CCCTAAACTTTTCC-AAAATTAC-TTTTAAC
1 CCTTAAAC-TTTCCAAAAATCACATTTT-AC
* *
63778 CCTCAAACTTTTCCAAAAATCATATTTTGA-
1 CCTTAAAC-TTTCCAAAAATCACATTTT-AC
* * * * * *
63808 CCTCAAACTTTTCCAAAATTAAAATATGAC
1 CCTTAAAC-TTTCCAAAAATCACATTTTAC
* * *
63838 CCCTAAACTTTTCC--AAATTATATTTTGAC
1 CCTTAAAC-TTTCCAAAAATCACATTTT-AC
*
63867 CCTTAAACTTTTCC-AAAATAACATTTTTAC
1 CCTTAAAC-TTTCCAAAAATCACA-TTTTAC
*
63897 CCTTAAAC-TTCTC-AAAATTACATTTTGAC
1 CCTTAAACTTTC-CAAAAATCACATTTT-AC
* * * *
63926 CCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCTTAAACTTTCCAAAAATCACATTTT-AC
* *
63956 TCTTAAACTTTTCC-AAAATCACATTTTTAT
1 CCTTAAAC-TTTCCAAAAATCACA-TTTTAC
*
63986 CC-TGAAC-TTCCAAAAATCACAATTTTAC
1 CCTTAAACTTTCCAAAAATCAC-ATTTTAC
* **
64014 CCTCAAAC--TAAAAAAATCACATTTTTAC
1 CCTTAAACTTTCCAAAAATCACA-TTTTAC
*** * *
64042 CCCCGAAC-TTCCAAAAAACATATTTATAC
1 CCTTAAACTTTCCAAAAATCACATTT-TAC
** *
64071 CCTCGAAC-TTCCTAAAATCACATTTTGAC
1 CCTTAAACTTTCCAAAAATCACATTTT-AC
* *
64100 TC-TAAACTTTCCAAAAATCACATTTTAA
1 CCTTAAACTTTCCAAAAATCACATTTTAC
64128 CCTTAAA
1 CCTTAAA
64135 TTCTTCGAAA
Statistics
Matches: 307, Mismatches: 56, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
27 5 0.02
28 60 0.20
29 116 0.38
30 104 0.34
31 22 0.07
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (29 bp):
CCTTAAACTTTCCAAAAATCACATTTTAC
Found at i:66422 original size:3 final size:3
Alignment explanation
Indices: 66414--66458 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
66404 CATTTAATGC
66414 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
66459 TCTTAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:67067 original size:51 final size:51
Alignment explanation
Indices: 67011--67113 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
67001 ATTTTGATCC
67011 TTAATTTTTTATTTAATTCGTTACAAATTATAAAGATATACGCTATTAATA
1 TTAATTTTTTATTTAATTCGTTACAAATTATAAAGATATACGCTATTAATA
67062 TTAATTTTTTATTTAATTCGTTACAAATTATAAAGATATACGCTATTAATA
1 TTAATTTTTTATTTAATTCGTTACAAATTATAAAGATATACGCTATTAATA
67113 T
1 T
67114 AGTAAAATTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.48
Consensus pattern (51 bp):
TTAATTTTTTATTTAATTCGTTACAAATTATAAAGATATACGCTATTAATA
Found at i:67307 original size:59 final size:60
Alignment explanation
Indices: 67228--67363 Score: 186
Period size: 59 Copynumber: 2.3 Consensus size: 60
67218 TTAATATAAC
* * * *
67228 ATTTGGTACCTG-AATTGATACTTTTTCCTAATTCGGTACTTGAACTTTTTTT-GATCCA
1 ATTTGGTACTTGAAATTGATACTTTTTCCTAATTCGGTACCTAAACTTTTTTTAGACCCA
* *
67286 ATTTGGTACTTGAAATTGATACTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGGACCCA
1 ATTTGGTACTTGAAATTGATACTTTTTCCTAATTCGGTACCTAAACTTTTTTTA-GACCCA
*
67347 ATTTGGTACTTAAAATT
1 ATTTGGTACTTGAAATT
67364 ATTAAATATT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
58 11 0.16
59 36 0.53
61 21 0.31
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (60 bp):
ATTTGGTACTTGAAATTGATACTTTTTCCTAATTCGGTACCTAAACTTTTTTTAGACCCA
Found at i:67642 original size:31 final size:31
Alignment explanation
Indices: 67562--67700 Score: 114
Period size: 31 Copynumber: 4.5 Consensus size: 31
67552 AGACCCCAAA
*
67562 AAGTTTAAGTACCAACTTAAGAAAAAAAGTGTTC
1 AAGTTTAAGTACCAAATT-AG-AAAAAAGTG-TC
**
67596 AA-TTTCGGTACCAAATTAGAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
* *
67626 AAGTTTAAGTATCAAATTGGACAAAAA-----
1 AAGTTTAAGTACCAAATTAGA-AAAAAGTGTC
*
67653 AA-TATTAAGTACCAAATTAGAAAAAATTGTC
1 AAGT-TTAAGTACCAAATTAGAAAAAAGTGTC
67684 AAGTTT-AGATACCAAAT
1 AAGTTTAAG-TACCAAAT
67701 ATTATATTAA
Statistics
Matches: 86, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
26 6 0.07
27 17 0.20
30 6 0.07
31 35 0.41
32 8 0.09
33 12 0.14
34 2 0.02
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:81236 original size:7 final size:7
Alignment explanation
Indices: 81224--81256 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
81214 CTTCAGAAGA
81224 TTTTTAT
1 TTTTTAT
81231 TTTTTA-
1 TTTTTAT
81237 TTTTTAT
1 TTTTTAT
*
81244 TTTATAT
1 TTTTTAT
81251 TTTTTA
1 TTTTTA
81257 AAAATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:81241 original size:13 final size:13
Alignment explanation
Indices: 81223--81254 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
81213 TCTTCAGAAG
*
81223 ATTTTTATTTTTT
1 ATTTTTATTTTAT
81236 ATTTTTATTTTAT
1 ATTTTTATTTTAT
81249 ATTTTT
1 ATTTTT
81255 TAAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
ATTTTTATTTTAT
Found at i:83457 original size:70 final size:70
Alignment explanation
Indices: 83378--83515 Score: 267
Period size: 70 Copynumber: 2.0 Consensus size: 70
83368 AGGCAGTTCT
*
83378 ATACTACTATGTTGCTACGACTCTTTGTTCTTCTTGAAGTAATTATGTTCAATGCATATATGAAC
1 ATACTACTATGTTGCTACGACTCTTTGTTCTTCTTGAAGTAATTATGTTCAATGCATATACGAAC
83443 ATACC
66 ATACC
83448 ATACTACTATGTTGCTACGACTCTTTGTTCTTCTTGAAGTAATTATGTTCAATGCATATACGAAC
1 ATACTACTATGTTGCTACGACTCTTTGTTCTTCTTGAAGTAATTATGTTCAATGCATATACGAAC
83513 ATA
66 ATA
83516 GGTATGGAGT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (70 bp):
ATACTACTATGTTGCTACGACTCTTTGTTCTTCTTGAAGTAATTATGTTCAATGCATATACGAAC
ATACC
Found at i:100395 original size:111 final size:111
Alignment explanation
Indices: 100199--100526 Score: 541
Period size: 111 Copynumber: 3.0 Consensus size: 111
100189 TTTTTAAAAT
* *
100199 CACTTTTTAAAAGCACTTCTCAAAAGCAATGTTAAACTAGCCCTTAACTTGTAAAAGGATTATGG
1 CACTTTTTAAAAGCACTTTTCAAAAGCAATGTTAAACTAGCTCTTAACTTGTAAAAGGATTATGG
* *
100264 GCTTTAGTCGATAGAAACGTATTGTTTTTGTTGATTGATTTCAAAG
66 GCTTTAGTCGATAGAGACGTATTGTTTTGGTTGATTGATTTCAAAG
* * * * *
100310 CACTTTTTAAAAACACTTTTCAAAAGCAATGATAAACTAGCTCTTAATTTATAAAAGGATTCTGG
1 CACTTTTTAAAAGCACTTTTCAAAAGCAATGTTAAACTAGCTCTTAACTTGTAAAAGGATTATGG
100375 GCTTTAGTCGATAGAGACGTATTGTTTTGGTTGATTGATTTCAAAG
66 GCTTTAGTCGATAGAGACGTATTGTTTTGGTTGATTGATTTCAAAG
*
100421 CACTTTTTAAAAGCA-TTTCTCAAAAGCAATGTTAAACTAACTCTTAACTTGTAAAAGGATTATG
1 CACTTTTTAAAAGCACTTT-TCAAAAGCAATGTTAAACTAGCTCTTAACTTGTAAAAGGATTATG
*
100485 GGCTTTAGTCGATAGAGACGTATTGTTTTGGTTGATTTATTT
65 GGCTTTAGTCGATAGAGACGTATTGTTTTGGTTGATTGATTT
100527 GGTGATTAAA
Statistics
Matches: 200, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
110 3 0.01
111 197 0.99
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (111 bp):
CACTTTTTAAAAGCACTTTTCAAAAGCAATGTTAAACTAGCTCTTAACTTGTAAAAGGATTATGG
GCTTTAGTCGATAGAGACGTATTGTTTTGGTTGATTGATTTCAAAG
Found at i:116032 original size:20 final size:20
Alignment explanation
Indices: 116007--116055 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
115997 AACAGAAGGA
116007 TTAACTAAAAAAATTTGGTT
1 TTAACTAAAAAAATTTGGTT
116027 TTAACTAAAAAAATTTGGTT
1 TTAACTAAAAAAATTTGGTT
116047 TTAACTAAA
1 TTAACTAAA
116056 TAATACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (20 bp):
TTAACTAAAAAAATTTGGTT
Found at i:117034 original size:97 final size:97
Alignment explanation
Indices: 116868--117061 Score: 345
Period size: 97 Copynumber: 2.0 Consensus size: 97
116858 GGGTCATATA
116868 TATGTATTGTACTAATGTTACACATATTCATCTAAATTTAAATTAAAATTTTCGATTCTACCCTA
1 TATGTATTGTACTAATGTTACACATATTCATCTAAATTTAAATTAAAATTTTCGATTCTACCCTA
116933 TCTGTCAACATATATAAATGAATAATTCTAAC
66 TCTGTCAACATATATAAATGAATAATTCTAAC
* * *
116965 TATGTATTGTATTAATGTTACATATATTCAT-TCAAATTTAAGTTAAAATTTTCGATTCTACCCT
1 TATGTATTGTACTAATGTTACACATATTCATCT-AAATTTAAATTAAAATTTTCGATTCTACCCT
117029 ATCTGTCAACATATATAAATGAATAATTCTAAC
65 ATCTGTCAACATATATAAATGAATAATTCTAAC
117062 ACATTTAAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
96 1 0.01
97 92 0.99
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (97 bp):
TATGTATTGTACTAATGTTACACATATTCATCTAAATTTAAATTAAAATTTTCGATTCTACCCTA
TCTGTCAACATATATAAATGAATAATTCTAAC
Found at i:134884 original size:21 final size:21
Alignment explanation
Indices: 134860--134901 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
134850 GTACAATCTC
*
134860 AAAATGTGGATCAAATTTAAAA
1 AAAAAGTGG-TCAAATTTAAAA
*
134882 AAAAAGTTGTCAAATTTAAA
1 AAAAAGTGGTCAAATTTAAA
134902 GACTAATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAGTGGTCAAATTTAAAA
Found at i:137583 original size:16 final size:17
Alignment explanation
Indices: 137552--137584 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
137542 GGTGAGATGC
137552 TGTTTTGGACTTGTGTA
1 TGTTTTGGACTTGTGTA
*
137569 TGTTTT-GATTTGTGTA
1 TGTTTTGGACTTGTGTA
137585 CTATTTGCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.12, C:0.03, G:0.27, T:0.58
Consensus pattern (17 bp):
TGTTTTGGACTTGTGTA
Found at i:139609 original size:35 final size:35
Alignment explanation
Indices: 139569--139638 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
139559 CTTCGAGATG
139569 CCATTAGTAGGAGATATGGACTGAAGGTTCCTCAT
1 CCATTAGTAGGAGATATGGACTGAAGGTTCCTCAT
139604 CCATTAGTAGGAGATATGGACTGAAGGTTCCTCAT
1 CCATTAGTAGGAGATATGGACTGAAGGTTCCTCAT
139639 GGTAAAGTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (35 bp):
CCATTAGTAGGAGATATGGACTGAAGGTTCCTCAT
Found at i:141830 original size:25 final size:24
Alignment explanation
Indices: 141773--141831 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
141763 AAAAATAGGT
* *
141773 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
141796 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
141820 TATTTTAATAAT
1 TATATT-ATAAT
141832 AATTATACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:141959 original size:58 final size:57
Alignment explanation
Indices: 141798--141966 Score: 182
Period size: 58 Copynumber: 2.9 Consensus size: 57
141788 TAATATTATA
* * * * *
141798 TATTATAATTTTTACT-AATTCATATTTTAATAATAATTATACTAAAAAAATTATTAAAT
1 TATTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATA-TTAAAATATAATTAAAT
* * *
141857 TATATATTATTTTT-TAAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAAT
1 TAT-TATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
*
141914 TAATTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 T-ATTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
141967 AACAATAATC
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
57 25 0.27
58 49 0.53
59 6 0.06
60 13 0.14
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (57 bp):
TATTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAAT
Found at i:151147 original size:13 final size:13
Alignment explanation
Indices: 151129--151154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
151119 AATTTTATTG
151129 AGTTATCTGTCAT
1 AGTTATCTGTCAT
151142 AGTTATCTGTCAT
1 AGTTATCTGTCAT
151155 TTCTTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
AGTTATCTGTCAT
Found at i:157702 original size:15 final size:15
Alignment explanation
Indices: 157652--157703 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
157642 GATTCGATTC
157652 AATTTTATA-AATAT
1 AATTTTATATAATAT
*
157666 AATTATTGATATAACAT
1 AATT-TT-ATATAATAT
* *
157683 CATTTTATATAATTT
1 AATTTTATATAATAT
157698 AATTTT
1 AATTTT
157704 TTTAAAACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.13
15 14 0.47
16 5 0.17
17 7 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (15 bp):
AATTTTATATAATAT
Found at i:158708 original size:44 final size:44
Alignment explanation
Indices: 158619--158706 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
158609 TAGTGTCGAG
* * *
158619 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTATGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
158663 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
158707 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.20, T:0.28
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:160392 original size:18 final size:18
Alignment explanation
Indices: 160369--160405 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
160359 TTTGTGATCA
160369 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
160387 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
160405 A
1 A
160406 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:160599 original size:37 final size:38
Alignment explanation
Indices: 160533--160611 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
160523 GTGTCATTAT
* *
160533 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGAGTCGATGAGATACTGGGTACCAC
* **
160571 TTTACTTCGGCTAG-GTCGATGAGATACTGGGTGTCAC
1 TTTACTTCGGATAGAGTCGATGAGATACTGGGTACCAC
160608 TTTA
1 TTTA
160612 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (38 bp):
TTTACTTCGGATAGAGTCGATGAGATACTGGGTACCAC
Found at i:162251 original size:34 final size:34
Alignment explanation
Indices: 162169--162253 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
162159 ATAATAAAAT
* *
162169 TAAATAAAAATTATAA-TAAAAATATAAAAATATT
1 TAAA-AAAAATTAAAATTAAAAATATAAAAATATG
***
162203 TAAAATTTATTAAAATTAAAAATATAAAAAT-TG
1 TAAAAAAAATTAAAATTAAAAATATAAAAATATG
162236 TAAAAAAAATATAAAATT
1 TAAAAAAAAT-TAAAATT
162254 TAATAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 15 0.37
34 26 0.63
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (34 bp):
TAAAAAAAATTAAAATTAAAAATATAAAAATATG
Found at i:162270 original size:19 final size:19
Alignment explanation
Indices: 162220--162263 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
162210 TATTAAAATT
162220 AAAAATATAAAAATTGTAAA
1 AAAAATAT-AAAATTGTAAA
*
162240 AAAAATATAAAATT-TAAT
1 AAAAATATAAAATTGTAAA
162258 AAAAAT
1 AAAAAT
162264 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 8 0.35
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATATAAAATTGTAAA
Found at i:162303 original size:9 final size:10
Alignment explanation
Indices: 162142--162347 Score: 55
Period size: 9 Copynumber: 21.0 Consensus size: 10
162132 ACGATGTGAT
162142 TAAAAATGATAA
1 TAAAAAT-AT-A
*
162154 TAATAATA-A
1 TAAAAATATA
* *
162163 TAAAATTAAA
1 TAAAAATATA
162173 TAAAAAT-TA
1 TAAAAATATA
*
162182 TAATAAAAATA
1 TAA-AAATATA
162193 TAAAAATAT-
1 TAAAAATATA
* *
162202 TTAAAATTTA
1 TAAAAATATA
*
162212 T-TAAA-AT-
1 TAAAAATATA
162219 TAAAAATATA
1 TAAAAATATA
* *
162229 -AAAATTGTA
1 TAAAAATATA
*
162238 -AAAAAAATA
1 TAAAAATATA
*
162247 T-AAAATTTAA
1 TAAAAATAT-A
*
162257 TAAAAATCGTA
1 TAAAAAT-ATA
*
162268 -AAAAAAACTTA
1 TAAAAATA--TA
162279 TAAGAAATATA
1 TAA-AAATATA
*
162290 GAAAAA-ATA
1 TAAAAATATA
* *
162299 TAAAATTTTA
1 TAAAAATATA
*
162309 T-AAAGT-TA
1 TAAAAATATA
162317 TAAGACAAT-TA
1 TAA-A-AATATA
162328 TAAAAATATA
1 TAAAAATATA
162338 -AAGAAATATA
1 TAA-AAATATA
162348 AAATTGTAAA
Statistics
Matches: 144, Mismatches: 29, Indels: 44
0.66 0.13 0.20
Matches are distributed among these distances:
7 1 0.01
8 7 0.05
9 58 0.40
10 40 0.28
11 25 0.17
12 9 0.06
13 4 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
TAAAAATATA
Done.