Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000127.1 Hibiscus syriacus cultivar Beakdansim tig00000227_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: 51848
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:6049 original size:17 final size:18
Alignment explanation
Indices: 6027--6060 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6017 TAAGTGATTT
6027 GATTAAAGAA-ATTAAAA
1 GATTAAAGAATATTAAAA
*
6044 GATTAATGAATATTAAA
1 GATTAAAGAATATTAAA
6061 GAAATTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (18 bp):
GATTAAAGAATATTAAAA
Found at i:9625 original size:22 final size:22
Alignment explanation
Indices: 9597--9652 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
9587 GTCGAGGGTT
9597 TCATAGGTCCTTCGGGACATAC
1 TCATAGGTCCTTCGGGACATAC
* *
9619 TCATAGGTCATTCGGGACATAT
1 TCATAGGTCCTTCGGGACATAC
*
9641 TCACAGGTCCTT
1 TCATAGGTCCTT
9653 AGAGATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (22 bp):
TCATAGGTCCTTCGGGACATAC
Found at i:15954 original size:22 final size:22
Alignment explanation
Indices: 15929--15991 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
15919 GTCGAGGGTT
15929 TCATAGGTCATTCGGGACATAC
1 TCATAGGTCATTCGGGACATAC
* *
15951 TCATAGGTCCTTCGGGACATAT
1 TCATAGGTCATTCGGGACATAC
* * *
15973 TCACAGGTCTTTAGGGACA
1 TCATAGGTCATTCGGGACA
15992 AATTTCATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (22 bp):
TCATAGGTCATTCGGGACATAC
Found at i:17073 original size:130 final size:128
Alignment explanation
Indices: 16775--17116 Score: 363
Period size: 130 Copynumber: 2.7 Consensus size: 128
16765 CGCAAAATGC
* * *
16775 ATCGATACACATATATA-AAGTATTGATACTTATAATTTCGAAATCTATTACTTTAAAGTAATAG
1 ATCGATA-ACATGTATATAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAG
** * * * * * *
16839 GTTTATTTACAATGAAAATGGTAAAAGTCTATCGATATAATGATAATAGGCATAAACATCAAGT
65 GTAAATTAACAATGTACACGATAAAAGTCTATCGATATAATGAAAATAGGCATAAACATCAAGT
* * ** *
16903 ATCGATACACATGTATA-AGGTATCGATACGTGGAATTTCGAAACCTAGTACTTTAAAGTAATAG
1 ATCGATA-ACATGTATATAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAG
* * **
16967 GTAAATTAACAATGTACACGATAAACGTTTCTA-CTGATATAATGAAAATAGGCGTAAATGTACA
65 GTAAATTAACAATGTACACGATAAAAG--TCTATC-GATATAATGAAAATAGGCATAAACAT-CA
17031 AGT
126 AGT
* *
17034 ATCGAT-AC-TGTCATATAAGTATCGATTA-TTATAATTTCGAAACATATTACTTTAAAGTATTA
1 ATCGATAACATGT-ATATAAGTATCGA-TACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
*
17096 GGTAAATTAACATTGTACACG
64 GGTAAATTAACAATGTACACG
17117 GTAATATATT
Statistics
Matches: 179, Mismatches: 28, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
128 78 0.44
129 6 0.03
130 82 0.46
131 13 0.07
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (128 bp):
ATCGATAACATGTATATAAGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGG
TAAATTAACAATGTACACGATAAAAGTCTATCGATATAATGAAAATAGGCATAAACATCAAGT
Found at i:18221 original size:29 final size:31
Alignment explanation
Indices: 18187--18250 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
18177 ATGGATTTGG
* *
18187 TTAGTGGCCAAAATATAAA-TTTTG-AAAGT
1 TTAGTGACCAAAATATAAACTTTAGAAAAGT
* *
18216 TTAGTGACGAAATTATAAACTTTAGAAAAGT
1 TTAGTGACCAAAATATAAACTTTAGAAAAGT
18247 TTAG
1 TTAG
18251 AAACTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.55
30 4 0.14
31 9 0.31
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (31 bp):
TTAGTGACCAAAATATAAACTTTAGAAAAGT
Found at i:20357 original size:23 final size:22
Alignment explanation
Indices: 20301--20361 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
20291 TAGCATTTTC
*
20301 GTAAGAATACTTTGTGTACTTG
1 GTAAGAGTACTTTGTGTACTTG
20323 G--AGTAGTACTTTGTGTACTATG
1 GTAAG-AGTACTTTGTGTACT-TG
20345 GTAAGAGTACTTTGTGT
1 GTAAGAGTACTTTGTGT
20362 GCGAGGATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 14 0.41
22 4 0.12
23 12 0.35
24 2 0.06
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (22 bp):
GTAAGAGTACTTTGTGTACTTG
Found at i:21739 original size:20 final size:20
Alignment explanation
Indices: 21714--21820 Score: 178
Period size: 20 Copynumber: 5.3 Consensus size: 20
21704 TTTTACGAAT
*
21714 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATCTGTAAA
*
21734 TCGCAATGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
21754 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
21774 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
21794 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
21814 TCGCAAC
1 TCGCAAC
21821 ACAGAAGTCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:21852 original size:20 final size:20
Alignment explanation
Indices: 21829--21975 Score: 145
Period size: 20 Copynumber: 7.3 Consensus size: 20
21819 ACACAGAAGT
*
21829 CAAATTTGCAATGCGATTTC
1 CAAATTCGCAATGCGATTTC
21849 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAATGCGATTTC
* * * *
21869 CAAATTCGCAACGTGAATCTG
1 CAAATTCGCAATGCG-ATTTC
* ** **
21890 TAAA-TCGCAACACAGAAGT-
1 CAAATTCGCAATGC-GATTTC
21909 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAATGCGATTTC
21929 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAATGCGATTTC
* * *
21949 CAAATTCGCAACGTGATTTA
1 CAAATTCGCAATGCGATTTC
21969 CAAATTC
1 CAAATTC
21976 ACAACACTAA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
19 6 0.06
20 92 0.88
21 7 0.07
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAATGCGATTTC
Found at i:21878 original size:80 final size:80
Alignment explanation
Indices: 21794--21964 Score: 333
Period size: 80 Copynumber: 2.1 Consensus size: 80
21784 AATCTGTAAA
*
21794 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTTGCAATGCGATTTCCAAATTCGCA
1 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
21859 ATGCGATTTCCAAAT
66 ATGCGATTTCCAAAT
21874 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
1 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
21939 ATGCGATTTCCAAAT
66 ATGCGATTTCCAAAT
21954 TCGCAACGTGA
1 TCGCAACGTGA
21965 TTTACAAATT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 90 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (80 bp):
TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
ATGCGATTTCCAAAT
Found at i:21918 original size:100 final size:98
Alignment explanation
Indices: 21774--21980 Score: 238
Period size: 100 Copynumber: 2.1 Consensus size: 98
21764 AATCTGTAAA
** *
21774 TCGCAACGCGAATCTGTAAATCGCAACGTGAATCTGTAAATCGCAACACAGAAGT-CAAATTTGC
1 TCGCAACGCGAATCTGTAAATCGCAACCAGAATC--TAAATCGCAACAC-GAAGTCCAAATTCGC
* *
21838 AATGCGATTTCCAAATTCGCAATGCGATTTCCAAAT
63 AATGCGATTTCCAAATTCGCAACGCGATTTACAAAT
* ** **
21874 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTC-AAATTCGCAATGCGATTTCCAAATTCGC
1 TCGCAACGCGAATCTGTAAATCGCAAC-CAGAA-TCTAAA-TCGCAACACGAAGTCCAAATTCGC
*
21938 AATGCGATTTCCAAATTCGCAACGTGATTTACAAAT
63 AATGCGATTTCCAAATTCGCAACGCGATTTACAAAT
*
21974 TCACAAC
1 TCGCAAC
21981 ACTAAATTTC
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
99 6 0.07
100 80 0.88
101 3 0.03
102 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (98 bp):
TCGCAACGCGAATCTGTAAATCGCAACCAGAATCTAAATCGCAACACGAAGTCCAAATTCGCAAT
GCGATTTCCAAATTCGCAACGCGATTTACAAAT
Found at i:21980 original size:20 final size:20
Alignment explanation
Indices: 21829--22008 Score: 141
Period size: 20 Copynumber: 8.9 Consensus size: 20
21819 ACACAGAAGT
* *
21829 CAAATTTGCAATGCGATTTC
1 CAAATTCGCAACGCGATTTC
*
21849 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAACGCGATTTC
* * *
21869 CAAATTCGCAACGTGAATCTG
1 CAAATTCGCAACGCG-ATTTC
* * **
21890 TAAA-TCGCAACACAGAAGT-
1 CAAATTCGCAACGC-GATTTC
*
21909 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAACGCGATTTC
*
21929 CAAATTCGCAATGCGATTTC
1 CAAATTCGCAACGCGATTTC
* *
21949 CAAATTCGCAACGTGATTTA
1 CAAATTCGCAACGCGATTTC
* * *
21969 CAAATTCACAACACTAAATTT-
1 CAAATTCGCAACGC--GATTTC
*
21990 CAAATTCGCAACTCGATTT
1 CAAATTCGCAACGCGATTT
22009 TTGAATTCGC
Statistics
Matches: 129, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
19 10 0.08
20 96 0.74
21 19 0.15
22 4 0.03
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:21981 original size:80 final size:80
Alignment explanation
Indices: 21794--22008 Score: 292
Period size: 80 Copynumber: 2.7 Consensus size: 80
21784 AATCTGTAAA
** * *
21794 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTTGCAATGCGATTTCCAAATTCGCA
1 TCGCAACGTGAATCTACAAATCACAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
21859 ATGCGATTTCCAAAT
66 ATGCGATTTCCAAAT
** *
21874 TCGCAACGTGAATCTGTAAATCGCAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
1 TCGCAACGTGAATCTACAAATCACAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
21939 ATGCGATTTCCAAAT
66 ATGCGATTTCCAAAT
* *
21954 TCGCAACGTG-ATTTACAAATTCACAACACTA-AATTTCAAATTCGCAACT-CGATTT
1 TCGCAACGTGAATCTACAAA-TCACAACAC-AGAA-GTCAAATTCGCAA-TGCGATTT
22009 TTGAATTCGC
Statistics
Matches: 125, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
79 6 0.05
80 99 0.79
81 19 0.15
82 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (80 bp):
TCGCAACGTGAATCTACAAATCACAACACAGAAGTCAAATTCGCAATGCGATTTCCAAATTCGCA
ATGCGATTTCCAAAT
Found at i:22017 original size:20 final size:20
Alignment explanation
Indices: 21992--22041 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
21982 CTAAATTTCA
*
21992 AATTCGCAACT-CGATTTTT
1 AATTCGCAACTACGAATTTT
22011 GAATTCGCAA-TACGAATTTT
1 -AATTCGCAACTACGAATTTT
22031 AATTTCGCAAC
1 AA-TTCGCAAC
22042 AGGTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
AATTCGCAACTACGAATTTT
Found at i:23808 original size:19 final size:20
Alignment explanation
Indices: 23786--23823 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23776 AATATTTTGT
23786 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
23805 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
23824 TACGCTTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:23836 original size:19 final size:20
Alignment explanation
Indices: 23794--23836 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
23784 GTTTCGAATT
* *
23794 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATACGCGTTA
*
23814 CGAAAAT-AAATACGCTTTA
1 CGAAAATAAAATACGCGTTA
23833 CGAA
1 CGAA
23837 TTTGACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (20 bp):
CGAAAATAAAATACGCGTTA
Found at i:25869 original size:20 final size:20
Alignment explanation
Indices: 25821--25882 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
25811 AACTTAAATC
*
25821 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
25841 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
25859 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
25878 AAAAT
1 AAAAT
25883 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:25984 original size:61 final size:60
Alignment explanation
Indices: 25877--26034 Score: 230
Period size: 61 Copynumber: 2.5 Consensus size: 60
25867 TTATATGATA
25877 TAAAATTAAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATT-AATATCTATAATAT-A-A-T-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
25942 TAAAATTAATATCTATAATATAATAAAATATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATAAAA-ATTAATATTTAATTTATTTAAAAAATTAATAT
*
26003 TAAAATTAAAATC-A-AATATAATATAAAATTAA
1 TAAAATTAATATCTATAATATAATA-AAAATTAA
26035 ATAAAACCTC
Statistics
Matches: 90, Mismatches: 1, Indels: 10
0.89 0.01 0.10
Matches are distributed among these distances:
59 14 0.16
60 8 0.09
61 45 0.50
62 1 0.01
63 1 0.01
64 14 0.16
65 7 0.08
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (60 bp):
TAAAATTAATATCTATAATATAATAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:25998 original size:24 final size:24
Alignment explanation
Indices: 25943--26004 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
25933 AATTAATATT
25943 AAAATTAATATCTATAATATAATAA
1 AAAATTAATAT-TATAATATAATAA
* * *
25968 AATATTAATATT-TAATTTATTTAA
1 AAAATTAATATTATAATATA-ATAA
25992 AAAATTAATATTA
1 AAAATTAATATTA
26005 AAATTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 6 0.19
24 15 0.48
25 10 0.32
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AAAATTAATATTATAATATAATAA
Found at i:27141 original size:26 final size:26
Alignment explanation
Indices: 27093--27143 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
27083 AAATATATAT
*
27093 TTAATATTTAAAATATTTTTTTAAAA
1 TTAATATTTAAAATATATTTTTAAAA
27119 TTAATATTTAAAA-AGTATTTTTAAA
1 TTAATATTTAAAATA-TATTTTTAAA
27144 TCAGTACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAATATTTAAAATATATTTTTAAAA
Found at i:29581 original size:22 final size:22
Alignment explanation
Indices: 29546--29603 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
29536 CAGCCAGCTG
**
29546 AAATGG-AGCGTTTGGTTGAGAA
1 AAATGGAAGC-TTTGGAAGAGAA
29568 AAATGGAAGCTTT-GAAGAGAA
1 AAATGGAAGCTTTGGAAGAGAA
* *
29589 AGATGAAAGCTTTGG
1 AAATGGAAGCTTTGG
29604 GGAGAACGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 17 0.57
22 10 0.33
23 3 0.10
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.24
Consensus pattern (22 bp):
AAATGGAAGCTTTGGAAGAGAA
Found at i:29609 original size:21 final size:21
Alignment explanation
Indices: 29563--29602 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29553 GCGTTTGGTT
*
29563 GAGAAAAATGGAAGCTTTGAA
1 GAGAAAAATGAAAGCTTTGAA
*
29584 GAGAAAGATGAAAGCTTTG
1 GAGAAAAATGAAAGCTTTG
29603 GGGAGAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (21 bp):
GAGAAAAATGAAAGCTTTGAA
Found at i:34206 original size:21 final size:19
Alignment explanation
Indices: 34175--34301 Score: 75
Period size: 21 Copynumber: 6.4 Consensus size: 19
34165 GCAAAGAAAC
*
34175 TAAAAATATAATGAAAATAA
1 TAAATATATAAT-AAAATAA
34195 TAAATAGTATAAATAAAATAA
1 TAAATA-TAT-AATAAAATAA
34216 TAAAATATATATATAAAATATA
1 T-AAATATATA-ATAAAATA-A
* * *
34238 AAAATGTATGTATATATAAATAC
1 TAAA--TATATA-ATA-AAATAA
*
34261 TAAATA-GTAAT--AATAA
1 TAAATATATAATAAAATAA
*
34277 TAAAAATA-AATAAAA-AA
1 TAAATATATAATAAAATAA
34294 TAAATATA
1 TAAATATA
34302 CATATAATAT
Statistics
Matches: 87, Mismatches: 9, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
16 12 0.14
17 9 0.10
18 2 0.02
19 2 0.02
20 9 0.10
21 27 0.31
22 9 0.10
23 12 0.14
24 5 0.06
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (19 bp):
TAAATATATAATAAAATAA
Found at i:34241 original size:29 final size:28
Alignment explanation
Indices: 34209--34375 Score: 76
Period size: 29 Copynumber: 5.8 Consensus size: 28
34199 TAGTATAAAT
34209 AAAATAATAAAATATATATATAAAATATA
1 AAAATAATAAAATATATA-ATAAAATATA
* **
34238 AAAAT-GTATGTATATATAAATACTAAATAGTA
1 AAAATAATA-AAATATAT-AATA--AAATA-TA
* *
34270 ATAATAATAAAA-ATA-AATAAAAAATA
1 AAAATAATAAAATATATAATAAAATATA
* * *
34296 AATATACATATAATAT-TAACTAAAAAATA
1 AAAATA-ATAAAATATATAA-TAAAATATA
** * *
34325 GTAATTATAGAAATATAAAATAAAATA-A
1 AAAATAATA-AAATATATAATAAAATATA
*
34353 ATAA-AATAAGAATATATATATAA
1 AAAATAATAA-AATATATA-ATAA
34376 CGTTAGGAAA
Statistics
Matches: 103, Mismatches: 21, Indels: 29
0.67 0.14 0.19
Matches are distributed among these distances:
26 7 0.07
27 19 0.18
28 17 0.17
29 40 0.39
30 3 0.03
31 8 0.08
32 7 0.07
33 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (28 bp):
AAAATAATAAAATATATAATAAAATATA
Found at i:34525 original size:23 final size:23
Alignment explanation
Indices: 34491--34537 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
34481 ACGCAAAGAA
34491 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
34514 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
34537 A
1 A
34538 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:36054 original size:106 final size:106
Alignment explanation
Indices: 35736--36794 Score: 1446
Period size: 106 Copynumber: 10.1 Consensus size: 106
35726 GTAAGTAGCA
* * * * ** * *
35736 TTGTTTTGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTT
1 TTGTCTTGGGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
* * *
35800 GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * *
35842 TTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-TT-TTT-
1 TTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
* * * *
35900 TTGACAATCAGCTG-CTCCTTCGTCGTGAAGTTGAGCTTGTG
66 TTGACAACCAGCGGTC-CCTTCGTCGTGAAGTTGAACTTGCG
* * *
35941 TTGTCTTGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTA
1 TTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
*
36006 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * * * *
36047 TTGTCTTGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTA
1 TTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
*
36112 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * *
36153 TTGTC-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTT
1 TTGTCTTGG-GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
*
36217 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCC
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
36259 TTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
1 TTGTCTTGG-GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
* *
36323 ATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCG
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * * *
36365 TTGTCTTGAGTCCAATATCCTTCGCTGTGAATTTAAAATTGGCTCTGAAATTTGGAAATTGTTTG
1 TTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
* *
36430 TTGACAACCAGGGGTCCCTTCGTCGTGAAGTTGAACTTGTG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * * *
36471 TTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
1 TTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
*
36536 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCG
66 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
36577 TTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTT
1 TTGTCTTGG-GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
* * *
36641 ATTGACAACCGGCGGTCCCTTCGTCGCGAAGTTGAACTTGCG
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
36683 TT-T-TTGGAGTCCAATATCCTTCG-TTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
1 TTGTCTTGG-GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT
* * *
36745 GTTGACAACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTG
65 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
36787 TTGTCTTG
1 TTGTCTTG
36795 AGTGGCACGA
Statistics
Matches: 860, Mismatches: 77, Indels: 32
0.89 0.08 0.03
Matches are distributed among these distances:
98 1 0.00
99 77 0.09
100 5 0.01
101 3 0.00
102 3 0.00
103 3 0.00
104 77 0.09
105 29 0.03
106 658 0.77
107 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
TTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTG
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
Found at i:36371 original size:318 final size:317
Alignment explanation
Indices: 35736--36797 Score: 1617
Period size: 318 Copynumber: 3.4 Consensus size: 317
35726 GTAAGTAGCA
* * * * *** *
35736 TTGTTTTGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTG
1 TTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTG
* * * *
35801 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCG
66 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTAGAGTCCAATATCCTTCG
* * * * *
35866 CTGTGAAGTTGAAATTGACTCTGAA-T--GAA-TT-TTT-TTGACAATCAGCTG-CTCCTTCGTC
131 TTGTGAAGTTGAAATTGGCTCTAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTC-CCTTCGTC
* * * *
35924 GTGAAGTTGAGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTG
195 GTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG
*
35988 AAATTGGGAAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCG
259 AAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* *
36047 TTGTCTTGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTA
1 TTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTG
* *
36112 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTAGAGTCCAATATCCTTCG
36177 TTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTC
131 TTGTGAAGTTGAAATTGGCTCT-AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTC
*
36242 GTGAAGTTGAACTTGCCTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
195 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
*
36307 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCG
260 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
* * *
36365 TTGTCTTGAGTCCAATATCCTTCGCTGTGAATTTAAAATTGGCTCTGAAATTTGGAAATTGTTTG
1 TTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTG
* *
36430 TTGACAACCAGGGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTAGAGTCCAATATCCTTCG
66 TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTAGAGTCCAATATCCTTCG
*
36495 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGTGGTCCCTTCGTC
131 TTGTGAAGTTGAAATTGGCTCT-AAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTC
36560 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
195 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
* * * *
36625 AATTGAGAAATTGTTTATTGACAACCGGCGGTCCCTTCGTCGCGAAGTTGAACTTGCG
260 AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
*
36683 TT-T-TTGGAGTCCAATATCCTTCGTT-TGAAGTTGAAATTGGCTCTGAAA-TTGAGAAGTTGTT
1 TTGTCTT-GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTG-GAAATTGTT
* *
36744 TGTTGACAACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGT
64 TGTTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTAGAGT
36798 GGCACGATAT
Statistics
Matches: 689, Mismatches: 51, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
311 136 0.20
312 2 0.00
313 1 0.00
315 6 0.01
316 83 0.12
317 25 0.04
318 435 0.63
319 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (317 bp):
TTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAATTGTTTG
TTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTAGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTCTAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
ATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCG
Found at i:37590 original size:22 final size:22
Alignment explanation
Indices: 37564--37640 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
37554 TTATGTTTGG
*
37564 TCAAAGGTTTGGCATTTTATGC
1 TCAAAGGTTTGGCATTTGATGC
37586 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
37608 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
37630 TCAACGGTTTG
1 TCAAAGGTTTG
37641 ATGGGGTAGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:38359 original size:171 final size:175
Alignment explanation
Indices: 38036--38381 Score: 585
Period size: 171 Copynumber: 2.0 Consensus size: 175
38026 TAAATAGGCC
* * *
38036 CAAACAAGTGTTTCAGTGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCATG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAAGATCAATTCATTATGATGCCTTCAATCATGTCATG
* *
38101 CTCAAAATGTCTCTCTCTTGATTCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
66 CTAAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
38166 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
131 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
*
38211 CAAACAAGTGTTTCAGGGTGTTGAACCAAAGATCAATTCATTATGATGTCTTCAATCATG-C-T-
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAAGATCAATTCATTATGATGCCTTCAATCATGTCATG
*
38273 C-AAAATATTTCTCTCTCTTGATGCTCTATGATCTTC-AGTGAAGTGATTCAGTGATTCGGGAAT
66 CTAAAA-ATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAAT
38336 GATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
130 GATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
38382 TTTTAGGGAA
Statistics
Matches: 163, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
171 76 0.47
172 29 0.18
173 1 0.01
174 1 0.01
175 56 0.34
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.37
Consensus pattern (175 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAAGATCAATTCATTATGATGCCTTCAATCATGTCATG
CTAAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:38427 original size:7 final size:7
Alignment explanation
Indices: 38415--38487 Score: 60
Period size: 8 Copynumber: 9.7 Consensus size: 7
38405 TTTTTGTCCC
38415 TTTTTCT
1 TTTTTCT
38422 TTTTTCTT
1 TTTTTC-T
38430 TTTGTTCT
1 TTT-TTCT
38438 TGTTTCTCT
1 T-TTT-TCT
38447 TTTTTC-
1 TTTTTCT
*
38453 -TTTGCT
1 TTTTTCT
38459 TTTTTGCT
1 TTTTT-CT
38467 TTTTTGCT
1 TTTTT-CT
38475 TCTTTTCT
1 T-TTTTCT
38483 TTTTT
1 TTTTT
38488 GTTCTTGATT
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
5 4 0.07
7 15 0.27
8 24 0.43
9 13 0.23
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:38430 original size:23 final size:25
Alignment explanation
Indices: 38404--38455 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
38394 TTTGCATGTG
38404 CTTTTTGTCCCT-TTT-TCTTTTTT
1 CTTTTTGTCCCTGTTTCTCTTTTTT
* *
38427 CTTTTTGTTCTTGTTTCTCTTTTTT
1 CTTTTTGTCCCTGTTTCTCTTTTTT
38452 CTTT
1 CTTT
38456 GCTTTTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 3 0.12
25 12 0.48
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (25 bp):
CTTTTTGTCCCTGTTTCTCTTTTTT
Found at i:41694 original size:23 final size:23
Alignment explanation
Indices: 41668--41712 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41658 CACCACAGCT
*
41668 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
41691 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
41713 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:41961 original size:149 final size:149
Alignment explanation
Indices: 41691--41994 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
41681 CGAAGTGCCC
41691 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
41756 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
41821 CATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
41840 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
41905 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
41970 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
41989 CGTAGA
1 CGTAGA
41995 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:42416 original size:19 final size:20
Alignment explanation
Indices: 42370--42406 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
42360 CCACGTTTGG
*
42370 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
42390 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
42407 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:47928 original size:22 final size:22
Alignment explanation
Indices: 47903--47946 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
47893 CACCACAGCT
*
47903 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
* *
47925 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
47947 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:48642 original size:19 final size:20
Alignment explanation
Indices: 48596--48632 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
48586 CCACGTTTGG
*
48596 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
48616 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
48633 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:50968 original size:13 final size:12
Alignment explanation
Indices: 50937--51000 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 12
50927 GCAAAGAAAC
50937 TAAA-ATAT-AA
1 TAAATATATAAA
50947 TAAA-A-ATAAA
1 TAAATATATAAA
50957 TAAATAGTATAAA
1 TAAATA-TATAAA
50970 TAAATA-ATAAA
1 TAAATATATAAA
*
50981 -AAATATATATA
1 TAAATATATAAA
*
50992 TAAAAATAT
1 TAAATATAT
51001 GAAAATGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
9 2 0.04
10 16 0.35
11 10 0.22
12 7 0.15
13 11 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
TAAATATATAAA
Found at i:51005 original size:22 final size:21
Alignment explanation
Indices: 50941--51026 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 21
50931 AGAAACTAAA
50941 ATATA-ATAAAAATAAATAAAT
1 ATATATATAAAAATAAA-AAAT
*
50962 AGTATAAATAAATAATAAAAAAT
1 A-TATATATAAA-AATAAAAAAT
*
50985 ATATATATAAAAATATGAAAAT
1 ATATATATAAAAATA-AAAAAT
* *
51007 GTATGTATAATATAATAAAA
1 ATATATATAA-A-AATAAAA
51027 TACTAAATAG
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
21 5 0.09
22 26 0.48
23 13 0.24
24 10 0.19
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATATATATAAAAATAAAAAAT
Found at i:51005 original size:24 final size:22
Alignment explanation
Indices: 50941--51005 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
50931 AGAAACTAAA
*
50941 ATATAATAAAAATA-AATAAAT
1 ATATAATAAAAATATAAAAAAT
*
50962 AGTATAA-ATAAATAATAAAAAAT
1 A-TATAATAAAAAT-ATAAAAAAT
*
50985 ATATATATAAAAATATGAAAA
1 ATATA-ATAAAAATATAAAAA
51006 TGTATGTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.17
22 10 0.29
23 14 0.40
24 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (22 bp):
ATATAATAAAAATATAAAAAAT
Found at i:51058 original size:24 final size:22
Alignment explanation
Indices: 50938--51059 Score: 60
Period size: 26 Copynumber: 5.3 Consensus size: 22
50928 CAAAGAAACT
50938 AAAATA-TAATAA-AAATAAAT-
1 AAAATAGT-ATAATAAATAAATA
50958 -AAATAGTATAAATAAAT-AATAA
1 AAAATAGTAT-AATAAATAAAT-A
50980 AAAATA-TATATATAAA-AATATGA
1 AAAATAGTATA-ATAAATAA-AT-A
*
51003 AAATGTATGTATAATATAATAAAATA
1 AAA-ATA-GTATAATA-AAT-AAATA
*
51029 CTAAATAGTAATAATAAATAAATGA
1 -AAAATAGT-ATAATAAATAAAT-A
51054 AAAATA
1 AAAATA
51060 ACATATAATA
Statistics
Matches: 79, Mismatches: 5, Indels: 32
0.68 0.04 0.28
Matches are distributed among these distances:
19 7 0.09
20 6 0.08
21 5 0.06
22 9 0.11
23 11 0.14
24 11 0.14
25 9 0.11
26 15 0.19
27 4 0.05
28 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAATAGTATAATAAATAAATA
Found at i:51203 original size:30 final size:31
Alignment explanation
Indices: 51137--51193 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
51127 TACGTTAGGA
* *
51137 AAATATAG-TAAAAAAAATAT-TAAATAAGT
1 AAATATAGATAAAAAATATATATATATAAGT
51166 AAATATAGATAAAAAATATATATATATA
1 AAATATAGATAAAAAATATATATATATA
51194 TATAATATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 11 0.46
31 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (31 bp):
AAATATAGATAAAAAATATATATATATAAGT
Found at i:51262 original size:22 final size:23
Alignment explanation
Indices: 51229--51274 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
51219 TACGCAAAGA
51229 AAATGAAAAAAATATAA-TAAAT
1 AAATGAAAAAAATATAATTAAAT
51251 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
51274 A
1 A
51275 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 13 0.59
23 6 0.27
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Done.