Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013757.1 Kokia drynarioides strain JFW-HI SEQ_128785, 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: 51230
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.33
Warning! 1919 characters in sequence are not A, C, G, or T
Found at i:2538 original size:15 final size:15
Alignment explanation
Indices: 2518--2550 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2508 ATACTTTAAA
2518 TATGATACAT-ATTAT
1 TATGATAC-TCATTAT
2533 TATGATACTCATTAT
1 TATGATACTCATTAT
2548 TAT
1 TAT
2551 CGTTCCACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (15 bp):
TATGATACTCATTAT
Found at i:3956 original size:22 final size:20
Alignment explanation
Indices: 3931--3978 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
3921 ATAAAATTAT
3931 TAAATATTAAAATTAAATAAAA
1 TAAATATTAAAA--AAATAAAA
*
3953 TAAATATTTAAAAAATAAAA
1 TAAATATTAAAAAAATAAAA
*
3973 AAAATA
1 TAAATA
3979 ATATGGACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAATATTAAAAAAATAAAA
Found at i:3971 original size:24 final size:22
Alignment explanation
Indices: 3931--3979 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
3921 ATAAAATTAT
* *
3931 TAAATATTAAAATTAAATAAAA
1 TAAATATTAAAAATAAAAAAAA
3953 TAAATATTTAAAAAATAAAAAAAA
1 TAAATA-TT-AAAAATAAAAAAAA
3977 TAA
1 TAA
3980 TATGGACCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 2 0.09
24 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATATTAAAAATAAAAAAAA
Found at i:6006 original size:47 final size:46
Alignment explanation
Indices: 5921--6017 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 46
5911 TTGTCTCTGG
* * * *
5921 TTTTTTTGTTGTTTAATGTTGTTTTTGCTCTCTTTTTTTGTTGCTA
1 TTTTTTTGTTGTTTAATGTTATGTTTGCTCACTGTTTTTGTTGCTA
*
5967 TTTTTGTTGTTGTTTTGATGTTATGTTTGCT-ACTGTTTTTGTTGCTA
1 TTTTT-TTGTTG-TTTAATGTTATGTTTGCTCACTGTTTTTGTTGCTA
6014 TTTT
1 TTTT
6018 GCTGTTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
46 5 0.11
47 24 0.55
48 15 0.34
ACGTcount: A:0.07, C:0.07, G:0.18, T:0.68
Consensus pattern (46 bp):
TTTTTTTGTTGTTTAATGTTATGTTTGCTCACTGTTTTTGTTGCTA
Found at i:6018 original size:35 final size:35
Alignment explanation
Indices: 5967--6040 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
5957 TTTGTTGCTA
* *
5967 TTTTTGTTGTTGTTTTGATGTTATGTTTGCTACTG
1 TTTTTGTTGCTATTTTGATGTTATGTTTGCTACTG
* * * *
6002 TTTTTGTTGCTATTTTGCTGTTATTTTTTCTATTG
1 TTTTTGTTGCTATTTTGATGTTATGTTTGCTACTG
6037 TTTT
1 TTTT
6041 GGTTTTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.68
Consensus pattern (35 bp):
TTTTTGTTGCTATTTTGATGTTATGTTTGCTACTG
Found at i:6028 original size:23 final size:22
Alignment explanation
Indices: 5953--6029 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
5943 TTTTGCTCTC
*
5953 TTTTTTTGTTGCTATTTTTGTTG
1 TTTTTTTGTTGCTA-TTTTGCTG
* * * *
5976 TTGTTTTGATGTTATGTTTGCTAC
1 TTTTTTTGTTGCTAT-TTTGCT-G
*
6000 TGTTTTTGTTGCTATTTTGCTG
1 TTTTTTTGTTGCTATTTTGCTG
6022 TTATTTTT
1 TT-TTTTT
6030 TCTATTGTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
22 2 0.05
23 27 0.68
24 11 0.28
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.68
Consensus pattern (22 bp):
TTTTTTTGTTGCTATTTTGCTG
Found at i:6067 original size:22 final size:22
Alignment explanation
Indices: 6014--6077 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
6004 TTTGTTGCTA
*
6014 TTTTGCTGTTATTTTTTCTAT-TG
1 TTTTG-TGTT-TTTTTTTTATGTG
*
6037 TTTTG-GTTTTTTTTTTATGTT
1 TTTTGTGTTTTTTTTTTATGTG
*
6058 TTTTGTGTTTTATTTTTATG
1 TTTTGTGTTTTTTTTTTATG
6078 CATTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.25
21 9 0.25
22 13 0.36
23 5 0.14
ACGTcount: A:0.08, C:0.03, G:0.14, T:0.75
Consensus pattern (22 bp):
TTTTGTGTTTTTTTTTTATGTG
Found at i:6083 original size:23 final size:21
Alignment explanation
Indices: 6037--6084 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
6027 TTTTCTATTG
* *
6037 TTTTGGTTTTTTTTTTATGTT
1 TTTTGGTTTTATTTTTATGAT
6058 TTTTGTGTTTTATTTTTATGCAT
1 TTTTG-GTTTTATTTTTATG-AT
6081 TTTT
1 TTTT
6085 TAATATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 13 0.57
23 5 0.22
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.77
Consensus pattern (21 bp):
TTTTGGTTTTATTTTTATGAT
Found at i:7002 original size:8 final size:8
Alignment explanation
Indices: 6989--7042 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
6979 TTTTTATTAA
6989 TTAATATT
1 TTAATATT
6997 TTAATATT
1 TTAATATT
7005 TTAATATT
1 TTAATATT
*
7013 TT-ATGTT
1 TTAATATT
*
7020 TTGATATT
1 TTAATATT
7028 TTGAAGT-TT
1 TT-AA-TATT
7037 TTAATA
1 TTAATA
7043 CTGTACTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 7 0.18
8 26 0.67
9 5 0.13
10 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (8 bp):
TTAATATT
Found at i:7021 original size:23 final size:23
Alignment explanation
Indices: 6973--7029 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
6963 AAGATGAAAC
*
6973 TTTTAAT-TTTTATTAATTAATA
1 TTTTAATATTTTAATAATTAATA
* * *
6995 TTTTAATATTTTAATATTTTATG
1 TTTTAATATTTTAATAATTAATA
*
7018 TTTTGATATTTT
1 TTTTAATATTTT
7030 GAAGTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTAATATTTTAATAATTAATA
Found at i:7026 original size:15 final size:16
Alignment explanation
Indices: 6989--7042 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
6979 TTTTTATTAA
6989 TTAATATTTTAATATT
1 TTAATATTTTAATATT
*
7005 TTAATATTTT-ATGTT
1 TTAATATTTTAATATT
*
7020 TTGATATTTTGAAGT-TT
1 TTAATATTTT-AA-TATT
7037 TTAATA
1 TTAATA
7043 CTGTACTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 13 0.41
16 10 0.31
17 8 0.25
18 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (16 bp):
TTAATATTTTAATATT
Found at i:7456 original size:20 final size:20
Alignment explanation
Indices: 7431--7469 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
7421 GATCTGCGCG
7431 GTTGGACCTTTTTGTTTCGA
1 GTTGGACCTTTTTGTTTCGA
7451 GTTGGACCTTTTTGTTTCG
1 GTTGGACCTTTTTGTTTCG
7470 CAAGGCTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (20 bp):
GTTGGACCTTTTTGTTTCGA
Found at i:12118 original size:4 final size:4
Alignment explanation
Indices: 12109--12135 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12099 TTTATATGTT
12109 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
12136 TCTATTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:15176 original size:15 final size:15
Alignment explanation
Indices: 15153--15189 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
15143 AACGACGATG
15153 GCGACGACAGCGACA
1 GCGACGACAGCGACA
*
15168 GCGATGACAGCGACA
1 GCGACGACAGCGACA
15183 GCGACGA
1 GCGACGA
15190 TCGGAGGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.35, T:0.03
Consensus pattern (15 bp):
GCGACGACAGCGACA
Found at i:15252 original size:15 final size:16
Alignment explanation
Indices: 15222--15252 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
15212 GAAGCATAAA
15222 AAAAGAAAGAAGAGAG
1 AAAAGAAAGAAGAGAG
15238 AAAAGAAAG-AGAGAG
1 AAAAGAAAGAAGAGAG
15253 GAGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAGAGAG
Found at i:15805 original size:29 final size:30
Alignment explanation
Indices: 15773--15989 Score: 210
Period size: 30 Copynumber: 7.3 Consensus size: 30
15763 TTGAAATTAT
* * *
15773 ATTTTAACCCTTAAAATTTT-TATAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATCAC
* *
15802 ATTTTAATCCC-TAAACATTTCCAAAATTAC
1 ATTTTAA-CCCTTAAACTTTTCCAAAATCAC
* * * *
15832 ACTTTGACCCCTAAAATTTTCC-AAAT-AC
1 ATTTTAACCCTTAAACTTTTCCAAAATCAC
** * *
15860 ATATTTAACCCCCAAACTTTTCTAAAATTAC
1 AT-TTTAACCCTTAAACTTTTCCAAAATCAC
*
15891 ATTTTAACCCTTAAACTTTTCCAAAATCAT
1 ATTTTAACCCTTAAACTTTTCCAAAATCAC
*
15921 ATTTTAA-CCTTAAACTTTTCCAAAATAAC
1 ATTTTAACCCTTAAACTTTTCCAAAATCAC
* * *
15950 ATTTTAACCCTCAAACTTCTCTAAAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATCAC
*
15980 ATTTTGACCC
1 ATTTTAACCC
15990 CCGAACTTCT
Statistics
Matches: 155, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
28 3 0.02
29 64 0.41
30 84 0.54
31 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTTCCAAAATCAC
Found at i:15850 original size:59 final size:58
Alignment explanation
Indices: 15766--15989 Score: 209
Period size: 59 Copynumber: 3.8 Consensus size: 58
15756 AACTTTTTTG
* * * *
15766 AAATTATATTTTAACCCTTAAAATTTT-TATAATCACATTTTAATCCCTAAACATTTCCA
1 AAATTACACTTTAACCCTTAAAATTTTCCA-AATCACATTTTAA-CCCTAAACTTTTCCA
* * * *
15825 AAATTACACTTTGACCCCTAAAATTTTCCAAAT-ACATATTTAACCCCCAAACTTTTCTA
1 AAATTACACTTTAACCCTTAAAATTTTCCAAATCACAT-TTTAA-CCCTAAACTTTTCCA
* * * *
15884 AAATTACATTTTAACCCTTAAACTTTTCCAAAATCATATTTTAACCTTAAACTTTTCCA
1 AAATTACACTTTAACCCTTAAAATTTTCC-AAATCACATTTTAACCCTAAACTTTTCCA
* * * * * * *
15943 AAATAACATTTTAACCCTCAAACTTCTCTAAAATCACATTTTGACCC
1 AAATTACACTTTAACCCTTAAAATTTTC-CAAATCACATTTTAACCC
15990 CCGAACTTCT
Statistics
Matches: 136, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
58 4 0.03
59 119 0.88
60 10 0.07
61 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.38
Consensus pattern (58 bp):
AAATTACACTTTAACCCTTAAAATTTTCCAAATCACATTTTAACCCTAAACTTTTCCA
Found at i:15947 original size:89 final size:88
Alignment explanation
Indices: 15796--15989 Score: 239
Period size: 89 Copynumber: 2.2 Consensus size: 88
15786 AAATTTTTAT
* *
15796 AATCACATTTTAATCCCTAAACATTTCCAAAATTACACTTTGACCCCTAAAATTTTCCAAAT-AC
1 AATCACATTTTAA-CCCTAAACATTTCCAAAATCACACTTTGAACCCTAAAATTTTCCAAATAAC
*
15860 ATATTTAACCCCCAAACTTTTCTAA
65 AT-TTTAACCCCCAAACTTCTCTAA
* * * * * *
15885 AATTACATTTTAACCCTTAAACTTTTCCAAAATCATA-TTTTAACCTTAAACTTTTCCAAAATAA
1 AATCACATTTTAACCC-TAAACATTTCCAAAATCACACTTTGAACCCTAAAATTTTCC-AAATAA
*
15949 CATTTTAACCCTCAAACTTCTCTAA
64 CATTTTAACCCCCAAACTTCTCTAA
*
15974 AATCACATTTTGACCC
1 AATCACATTTTAACCC
15990 CCGAACTTCT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 19 0.21
89 67 0.74
90 4 0.04
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.36
Consensus pattern (88 bp):
AATCACATTTTAACCCTAAACATTTCCAAAATCACACTTTGAACCCTAAAATTTTCCAAATAACA
TTTTAACCCCCAAACTTCTCTAA
Found at i:15976 original size:30 final size:30
Alignment explanation
Indices: 15754--16006 Score: 194
Period size: 30 Copynumber: 8.5 Consensus size: 30
15744 AAGAGGTCCC
* * * *
15754 CAAACTTTTTTGAAATTATATTTTAACCCT
1 CAAACTTTTCTAAAATCACATTTTAACCCT
* * *
15784 TAAAATTTT-TATAATCACATTTTAATCCCT
1 CAAACTTTTCTAAAATCACATTTTAA-CCCT
* * * * *
15814 -AAACATTTCCAAAATTACACTTTGACCC-
1 CAAACTTTTCTAAAATCACATTTTAACCCT
* * *
15842 CTAAAATTTTC-CAAAT-ACATATTTAACCCC
1 C-AAACTTTTCTAAAATCACAT-TTTAACCCT
*
15872 CAAACTTTTCTAAAATTACATTTTAACCCT
1 CAAACTTTTCTAAAATCACATTTTAACCCT
* * *
15902 TAAACTTTTCCAAAATCATATTTTAA-CCT
1 CAAACTTTTCTAAAATCACATTTTAACCCT
* * *
15931 TAAACTTTTCCAAAATAACATTTTAACCCT
1 CAAACTTTTCTAAAATCACATTTTAACCCT
* * *
15961 CAAACTTCTCTAAAATCACATTTTGACCCC
1 CAAACTTTTCTAAAATCACATTTTAACCCT
* *
15991 CGAACTTCTCTAAAAT
1 CAAACTTTTCTAAAAT
16007 TTCATTTTCA
Statistics
Matches: 180, Mismatches: 34, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
28 3 0.02
29 67 0.37
30 106 0.59
31 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
CAAACTTTTCTAAAATCACATTTTAACCCT
Found at i:16854 original size:25 final size:25
Alignment explanation
Indices: 16820--16872 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
16810 CTACTCCACT
*
16820 AGGGGCAATAAGAGAGTCAAGCCAA
1 AGGGCCAATAAGAGAGTCAAGCCAA
16845 AGGGCCAATAAGAGAGTCAAGCCAA
1 AGGGCCAATAAGAGAGTCAAGCCAA
16870 AGG
1 AGG
16873 TCAATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.32, T:0.08
Consensus pattern (25 bp):
AGGGCCAATAAGAGAGTCAAGCCAA
Found at i:20725 original size:22 final size:25
Alignment explanation
Indices: 20700--20751 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 25
20690 ATTTGCGCTA
20700 TGTGCGCCTACT-GATTGCA-T-TG
1 TGTGCGCCTACTGGATTGCACTATG
*
20722 TGTGTGCCTACTGGATTGCACTATG
1 TGTGCGCCTACTGGATTGCACTATG
20747 TGTGC
1 TGTGC
20752 TTACTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 1 0.04
25 6 0.24
ACGTcount: A:0.13, C:0.21, G:0.29, T:0.37
Consensus pattern (25 bp):
TGTGCGCCTACTGGATTGCACTATG
Found at i:20748 original size:23 final size:22
Alignment explanation
Indices: 20692--20756 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
20682 GCGCGCCAAT
* *
20692 TTGCGCTATGTGCGCCTACTGA
1 TTGCACTATGTGTGCCTACTGA
* *
20714 TTGCATTGTGTGTGCCTACTGGA
1 TTGCACTATGTGTGCCTACT-GA
*
20737 TTGCACTATGTGTGCTTACT
1 TTGCACTATGTGTGCCTACT
20757 ATTAAGTACT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (22 bp):
TTGCACTATGTGTGCCTACTGA
Found at i:23212 original size:17 final size:17
Alignment explanation
Indices: 23109--23176 Score: 100
Period size: 17 Copynumber: 4.0 Consensus size: 17
23099 TAAATCCAAC
* *
23109 TTTTAATTTTAAATTTG
1 TTTTAAATTTAAATTTA
23126 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
23143 TTTGAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
23160 TTTTAAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
23177 GATTTAGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:23247 original size:6 final size:6
Alignment explanation
Indices: 23127--23213 Score: 74
Period size: 6 Copynumber: 15.0 Consensus size: 6
23117 TTAAATTTGT
* *
23127 TTTAAA TTTAAA TTT--A TTTGAAA TTTAAA TTT-AT TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
23173 TTTAGA TTTAGA TTTAGA TTTAAG TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
23214 ATTTGAAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
4 4 0.06
5 8 0.12
6 52 0.76
7 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:23681 original size:26 final size:26
Alignment explanation
Indices: 23640--23701 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
23630 CCCTTTGTTG
*
23640 AGCATTCAAAATCAATACAAA-AAAT
1 AGCATTCAAAAGCAATACAAATAAAT
*
23665 AGGCATTCAAAAGCAATACAAATAGAT
1 A-GCATTCAAAAGCAATACAAATAAAT
23692 AGCATTCAAA
1 AGCATTCAAA
23702 GCCAATAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 1 0.03
26 28 0.85
27 4 0.12
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (26 bp):
AGCATTCAAAAGCAATACAAATAAAT
Found at i:23707 original size:26 final size:24
Alignment explanation
Indices: 23640--23708 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 24
23630 CCCTTTGTTG
*
23640 AGCATTCAAAATCAATACAAAAAAT
1 AGCATTC-AAAGCAATACAAAAAAT
*
23665 AGGCATTCAAAAGCAATACAAATAGAT
1 A-GCATTC-AAAGCAATACAAA-AAAT
23692 AGCATTCAAAGCCAATA
1 AGCATTCAAAG-CAATA
23709 GAGAAGAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.13
26 30 0.77
27 4 0.10
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (24 bp):
AGCATTCAAAGCAATACAAAAAAT
Found at i:25143 original size:29 final size:28
Alignment explanation
Indices: 25006--25147 Score: 81
Period size: 29 Copynumber: 4.8 Consensus size: 28
24996 TACCCTAGAT
*
25006 CTTTCCAAAAATTATCGTTTTA-CCCCTAAA
1 CTTT-CAAAAATTA-CATTTTACCCCCT-AA
* * * *
25036 CATCCAAAAATAACAATTTTACCCTC-AA
1 CTTTCAAAAATTAC-ATTTTACCCCCTAA
* * *
25064 GCATTCAAAAAATACATTTTTGCCCCCTAA
1 -CTTTCAAAAATTACA-TTTTACCCCCTAA
* * * *
25094 ATTTCCAAAGATGATATTTTTACCCCCTAA
1 CTTT-CAAAAATTACA-TTTTACCCCCTAA
25124 CTTTCAAAAATTACCATTTTACCC
1 CTTTCAAAAATTA-CATTTTACCC
25148 TCGAGCATCC
Statistics
Matches: 84, Mismatches: 21, Indels: 15
0.70 0.17 0.12
Matches are distributed among these distances:
28 4 0.05
29 49 0.58
30 31 0.37
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (28 bp):
CTTTCAAAAATTACATTTTACCCCCTAA
Found at i:25143 original size:30 final size:29
Alignment explanation
Indices: 25067--25147 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 29
25057 CCCTCAAGCA
* *
25067 TTCAAAAAATACATTTTTGCCCCCTAAAT
1 TTCAAAAATTACATTTTTACCCCCTAAAT
* * * *
25096 TTCCAAAGATGATATTTTTACCCCCTAACT
1 TT-CAAAAATTACATTTTTACCCCCTAAAT
25126 TTCAAAAATTACCA-TTTTACCC
1 TTCAAAAATTA-CATTTTTACCC
25148 TCGAGCATCC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 17 0.41
30 24 0.59
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
TTCAAAAATTACATTTTTACCCCCTAAAT
Found at i:27620 original size:49 final size:49
Alignment explanation
Indices: 27548--28259 Score: 406
Period size: 49 Copynumber: 14.5 Consensus size: 49
27538 GAAGATATGG
* * *
27548 AGGGAAAGGTTTAAGTTGCAACGGCGAACCTTCTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * * * *
27597 AGGGAAAGATTTAAGCCACAACGGCGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * * *
27646 AGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * * * * *
27695 AGGCAAAGATGTAAG-CTGTAATGGCAAATCTAGTA-C-CATGAAGATATGA
1 AGGGAAAGATTTAAGTC-GCAACGGCGAACCTTGTACCTCA-GAA-ACATGA
* * * * *
27744 AGGGAAAGGTTTAAGTCGCAATGGCGAACCCTGTACCTCAGAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * ** * * * * *
27793 AGGGAAAGATGTAAG-CTGAAATGGAAAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTC-GCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * * ** *
27842 AGGGAAAGATTTAAGTCGTAATGGCGAGCCTTGTACCTTGGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * * * * *
27891 AGGGAAAGATTTAAGCCGCAACAGTGAATCTAGTACCAC-GAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * **
27940 AGGGAAAGGTTTAAGTCACAACAACGAACCTTGTACCTCA-AAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAA-CATGA
** * * * * *
27989 AGGGAAAGATTTAAGTCGCAACGATGAATCCAT-TACCACA-AGGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGA-AACATGA
* * * *
28038 AGAGAAAGGTTTAAGTCGCAACGGCGAATCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* ** * * * *
28087 AGGGAAAGATTTAAGCCGCAACGATGAATCTAGTACCAT-A-AAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACC-TCAGAA-ACATGA
* * * * *
28136 AGGGAAAGTTTTAAGTCGTAACGGTGAACCTTGTACCTCATAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
* * * * * * *
28185 AGGGAAAAAATTTAAGTCGCAATGACGAATCTAGTACCAC-GAATATATGA
1 AGGG-AAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACATGA
* * * *
28235 AGGGAAAAATATAAGCCGTAACGGC
1 AGGGAAAGATTTAAGTCGCAACGGC
28260 AAATCCAGTA
Statistics
Matches: 492, Mismatches: 146, Indels: 50
0.72 0.21 0.07
Matches are distributed among these distances:
47 2 0.00
48 21 0.04
49 413 0.84
50 54 0.11
51 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (49 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
Found at i:27703 original size:98 final size:98
Alignment explanation
Indices: 27532--28241 Score: 861
Period size: 98 Copynumber: 7.2 Consensus size: 98
27522 CAGGTTTCAT
* *
27532 TACCACGAAGATATGGAGGGAAAGGTTTAAGT-TGCAACGGCGAACCTTCTACCTCAGAAACATG
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCT-CAACGGCGAACCTTGTACCTCAGAAGCATG
*
27596 AAGGGAAAGATTTAAGCCACAACGGCGAATCTAG
65 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
*
27630 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATAA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATGA
* * * * * *
27695 AGGCAAAGATGTAAGCTGTAATGGCAAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * *
27728 TACCATGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCCTGTACCTCAGAAGCATAA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATGA
* * * * **
27793 AGGGAAAGATGTAAGCTGAAATGGAAAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * **
27826 TACCACGAAGATATGGAGGGAAAGATTTAAGTCGT-AATGGCGAGCCTTGTACCTTGGAAGCATG
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTC-TCAACGGCGAACCTTGTACCTCAGAAGCATG
* *
27890 AAGGGAAAGATTTAAGCCGCAACAGTGAATCTAG
65 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* ** *
27924 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCACAACAACGAACCTTGTACCTCAAAAGCATGA
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATGA
* ** * *
27989 AGGGAAAGATTTAAGTCGCAACGATGAATCCAT
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * *
28022 TACCAC-AAGGATATGGAGAGAAAGGTTTAAGTCGCAACGGCGAATCTTGTACCTCAGAAGCATG
1 TACCACGAA-GATATGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATG
**
28086 AAGGGAAAGATTTAAGCCGCAACGATGAATCTAG
65 AAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
** * * *
28120 TACCATAAAGATATGGAGGGAAAGTTTTAAGTCGT-AACGGTGAACCTTGTACCTCATAAGCATG
1 TACCACGAAGATATGGAGGGAAAGGTTTAAGTC-TCAACGGCGAACCTTGTACCTCAGAAGCATG
* * * *
28184 AAGGGAAAAAATTTAAGTCGCAATGACGAATCTAG
65 AAGGG-AAAGATTTAAGCCGCAACGGCGAATCTAG
* *
28219 TACCACGAATATATGAAGGGAAA
1 TACCACGAAGATATGGAGGGAAA
28242 AATATAAGCC
Statistics
Matches: 533, Mismatches: 72, Indels: 13
0.86 0.12 0.02
Matches are distributed among these distances:
97 2 0.00
98 484 0.91
99 47 0.09
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (98 bp):
TACCACGAAGATATGGAGGGAAAGGTTTAAGTCTCAACGGCGAACCTTGTACCTCAGAAGCATGA
AGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
Found at i:28319 original size:148 final size:148
Alignment explanation
Indices: 28047--28321 Score: 329
Period size: 148 Copynumber: 1.9 Consensus size: 148
28037 GAGAGAAAGG
* * * * * * *
28047 TTTAAGTCGCAACGGCGAATCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGAT
1 TTTAAGTCGCAACGACGAATCTAGTACCACAGAAACATGAAGGGAAAAATATAAGCCGCAACGAC
* * * * * * *
28112 GAATCTAGTACCATAAAGATATGGAGGGAAAGTTTTAAGTCGTAACGGTGAACCTTGTACCTCAT
66 AAATCCAGTACCATAAAGATATGGAGGGAAAGTGTTAAGACGCAACGGCGAACCCTGTACCTCAT
28177 AAGCATGAAGGGAAAAAA
131 AAGCATGAAGGGAAAAAA
* * * *
28195 TTTAAGTCGCAATGACGAATCTAGTACCAC-GAATATATGAAGGGAAAAATATAAGCCGTAACGG
1 TTTAAGTCGCAACGACGAATCTAGTACCACAGAA-ACATGAAGGGAAAAATATAAGCCGCAACGA
* * *
28259 CAAATCCAGTACCATGAAGATATGGAGGGAAAG-GTTACGACTGCAATGGCGAACCCTGTACCT
65 CAAATCCAGTACCATAAAGATATGGAGGGAAAGTGTTAAGAC-GCAACGGCGAACCCTGTACCT
28322 TAGAAACATG
Statistics
Matches: 104, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
147 8 0.08
148 96 0.92
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.21
Consensus pattern (148 bp):
TTTAAGTCGCAACGACGAATCTAGTACCACAGAAACATGAAGGGAAAAATATAAGCCGCAACGAC
AAATCCAGTACCATAAAGATATGGAGGGAAAGTGTTAAGACGCAACGGCGAACCCTGTACCTCAT
AAGCATGAAGGGAAAAAA
Found at i:28638 original size:45 final size:46
Alignment explanation
Indices: 28570--28673 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
28560 CCCCGATCAT
* * * *
28570 GGGGCATATTGAAGCCACCATCCAATC-TTTACCCCTAAGTCAAGA
1 GGGGCAAATTGAAACCACAATCCAATCTTTTACCCCTAAATCAAGA
*
28615 GGGGCTAATTGAAACCACAATCCAATCTTTTACCCCTAAATCAAGA
1 GGGGCAAATTGAAACCACAATCCAATCTTTTACCCCTAAATCAAGA
28661 GGGGCAAATTGAA
1 GGGGCAAATTGAA
28674 GCTAACATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 23 0.44
46 29 0.56
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (46 bp):
GGGGCAAATTGAAACCACAATCCAATCTTTTACCCCTAAATCAAGA
Found at i:30661 original size:30 final size:30
Alignment explanation
Indices: 30623--30912 Score: 284
Period size: 30 Copynumber: 9.8 Consensus size: 30
30613 AAAGGTCCCC
* *
30623 AAACTTTTCTAAAATTATATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * * *
30653 AAAATTTTCTAAAATCACATTTTAAACCTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* *
30683 AAACTTTTCCAAAATTACATTTTGACCC-C
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
30712 AAACTTTTTCAAAATTATATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* *
30742 AAACTTTTCCAAAAGTACATTTTAACCTTT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
30772 AAACTTGTCCAAAATCATATTTTGACACCC-T
1 AAACTTTTCCAAAATTACATTTT-A-ACCCTT
* *
30803 AAACTTTTCC-AAATTACATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
30832 AAACTTTTCCAAAATCATATTTTAACCC-C
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* **
30861 AAAC-TTTCCAAAATCACATTTTAACCCCC
1 AAACTTTTCCAAAATTACATTTTAACCCTT
* * *
30890 GAACTTTTCTAAAATCACATTTT
1 AAACTTTTCCAAAATTACATTTT
30913 GAGTCCCGAA
Statistics
Matches: 218, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
28 26 0.12
29 44 0.20
30 134 0.61
31 11 0.05
32 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTAACCCTT
Found at i:30697 original size:60 final size:60
Alignment explanation
Indices: 30623--30912 Score: 329
Period size: 60 Copynumber: 4.9 Consensus size: 60
30613 AAAGGTCCCC
* * * * * *
30623 AAACTTTTCTAAAATTATATTTTAACCCTTAAAATTTTCTAAAATCACATTTTAAACCTT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCATATTTTAAACCCT
* * *
30683 AAACTTTTCCAAAATTACATTTTGACCCC-AAACTTTT-TCAAAATTATATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCT-AAAATCATATTTTAAACCCT
* ** * * *
30742 AAACTTTTCCAAAAGTACATTTTAACCTTTAAACTTGTCCAAAATCATATTTTGACACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCATATTTT-AAACCCT
* * *
30803 AAACTTTTCC-AAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATTTT-AACCCC
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCATATTTTAAACCCT
* ** *
30861 AAAC-TTTCCAAAATCACATTTTAACCCCCGAACTTTTCTAAAATCACATTTT
1 AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCATATTTT
30913 GAGTCCCGAA
Statistics
Matches: 194, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
57 5 0.03
58 45 0.23
59 48 0.25
60 81 0.42
61 15 0.08
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (60 bp):
AAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTTCTAAAATCATATTTTAAACCCT
Found at i:30727 original size:89 final size:87
Alignment explanation
Indices: 30619--30904 Score: 351
Period size: 89 Copynumber: 3.2 Consensus size: 87
30609 CTCAAAAGGT
* * *
30619 CCCCAAACTTTTCTAAAATTATATTTTAACCCTTAAAATTTTCTAAAATCACATTTTAAACCTTA
1 CCCCAAACTTTTC-AAAATTATATTTTAACCCCTAAACTTTTCCAAAATCACATTTT-AACCTTA
*
30684 AACTTTTCCAAAATTACATTTTGA
64 AACTTTTCCAAAATCACATTTTGA
30708 CCCCAAACTTTTTCAAAATTATATTTTAACCCCTAAACTTTTCCAAAAGT-ACATTTTAACCTTT
1 CCCCAAAC-TTTTCAAAATTATATTTTAACCCCTAAACTTTTCCAAAA-TCACATTTTAACC-TT
* *
30772 AAACTTGTCCAAAATCATATTTTGA
63 AAACTTTTCCAAAATCACATTTTGA
* * * * **
30797 CACCCTAAACTTTTCCAAATTACATTTTGACCCCTAAACTTTTCCAAAATCATATTTTAACCCCA
1 C-CCC-AAACTTTTCAAAATTATATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCTTA
*
30862 AAC-TTTCCAAAATCACATTTTAA
64 AACTTTTCCAAAATCACATTTTGA
*
30885 CCCCCGAACTTTTCTAAAAT
1 -CCCCAAACTTTTC-AAAAT
30905 CACATTTTGA
Statistics
Matches: 172, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
87 8 0.05
88 28 0.16
89 77 0.45
90 55 0.32
91 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (87 bp):
CCCCAAACTTTTCAAAATTATATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCTTAAA
CTTTTCCAAAATCACATTTTGA
Found at i:35974 original size:16 final size:16
Alignment explanation
Indices: 35953--35995 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
35943 ATGAAAAATA
35953 ATATTAAAATTTTGGT
1 ATATTAAAATTTTGGT
35969 ATATTAAAATTTTGGT
1 ATATTAAAATTTTGGT
35985 ATATTAAAATT
1 ATATTAAAATT
35996 ACAAAATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (16 bp):
ATATTAAAATTTTGGT
Found at i:37956 original size:20 final size:20
Alignment explanation
Indices: 37921--37958 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37911 AAAATTTACT
*
37921 CATAATTTAATGATTAATGA
1 CATAATTTAATCATTAATGA
*
37941 CATAATTTACTCATTAAT
1 CATAATTTAATCATTAAT
37959 TTTTTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (20 bp):
CATAATTTAATCATTAATGA
Found at i:42093 original size:17 final size:17
Alignment explanation
Indices: 42071--42104 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42061 CTAAGAATTT
42071 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
42088 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
42105 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:42967 original size:23 final size:23
Alignment explanation
Indices: 42935--42988 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
42925 CCATCCTTGT
* *
42935 TGACTAGACCTTTTAGAAGCTAC
1 TGACTGGACCTTCTAGAAGCTAC
*
42958 TGACTGGACCTTCTAGAAGCTGC
1 TGACTGGACCTTCTAGAAGCTAC
42981 TGACTGGA
1 TGACTGGA
42989 TGCCACGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
TGACTGGACCTTCTAGAAGCTAC
Found at i:43300 original size:41 final size:41
Alignment explanation
Indices: 43239--43320 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
43229 ACACATAGTC
* *
43239 ATCGGACCTCTTAATTCGTAAAGGATTCATATACCCACGAT
1 ATCGGACCTCATAATCCGTAAAGGATTCATATACCCACGAT
*
43280 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGAT
1 ATCGGACCTCATAATCCGTAAAGGATTCATATACCCACGAT
43321 CACACATAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (41 bp):
ATCGGACCTCATAATCCGTAAAGGATTCATATACCCACGAT
Found at i:43327 original size:93 final size:98
Alignment explanation
Indices: 43217--43469 Score: 320
Period size: 104 Copynumber: 2.6 Consensus size: 98
43207 ATTTCATTTA
* *
43217 ATACTCACAATGACACATAGTCATCGGACCTCTTAATTCGTAAAGGATTCATATAC-C-CAC-GA
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACACACACAGA
*
43279 -T-ATCGGACCTCATAATCCGTAAAGGATTCAT
66 GTCATCGGACCTCAAAATCCGTAAAGGATTCAT
* *
43310 ATACTCACGATCACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCA
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTC--ATA-T-AC-A-CA
*
43375 CACATAGTCATCGGACCTCAAAATCCGTAAAGGATTCAT
60 CACAGAGTCATCGGACCTCAAAATCCGTAAAGGATTCAT
* * *
43414 ATACTCATGCTGACACATAGTCGTCGGACCTCATAA-TCTGTAAAGGATTCATATAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATTC-GTAAAGGATTCATATAC
43470 TCATGATGAC
Statistics
Matches: 137, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
93 46 0.34
95 3 0.02
96 1 0.01
97 2 0.01
100 3 0.02
101 4 0.03
102 4 0.03
103 2 0.01
104 72 0.53
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.26
Consensus pattern (98 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACACACACAGA
GTCATCGGACCTCAAAATCCGTAAAGGATTCAT
Found at i:43358 original size:52 final size:52
Alignment explanation
Indices: 43280--43496 Score: 353
Period size: 52 Copynumber: 4.2 Consensus size: 52
43270 TACCCACGAT
43280 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
1 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
43332 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
1 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
* * * *
43384 ATCGGACCTCAAAATCCGTAAAGGATTCATATACTCATGCTGACACATAGTC
1 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
* * * * *
43436 GTCGGACCTCATAATCTGTAAAGGATTCATATACTCATGATGACACATAATC
1 ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
43488 ATCGGACCT
1 ATCGGACCT
43497 TTTTCATTTA
Statistics
Matches: 155, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 155 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (52 bp):
ATCGGACCTCATAATCCGTAAAGGATTCATATACTCACGATCACACATAGTC
Found at i:43766 original size:13 final size:13
Alignment explanation
Indices: 43750--43774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43740 CCAAATTCTT
43750 TAATTAAATCATA
1 TAATTAAATCATA
43763 TAATTAAATCAT
1 TAATTAAATCAT
43775 TTAACATTAT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATTAAATCATA
Found at i:45574 original size:149 final size:149
Alignment explanation
Indices: 45354--45661 Score: 374
Period size: 150 Copynumber: 2.1 Consensus size: 149
45344 TCCCTAGATT
* * * * * *
45354 TTCAAATATTACGATTTTGACTTGTTTTTCTGTTTTTTATTATTATTTTTACCTACAATTTGATT
1 TTCAAA-AATACGATTTCGACTCGTTTTTCTATTTTTTATTATTATTTTTACCTAAAATTTAATT
* * * *
45419 TTTTTTTAATTTAGTCCTTAAGA-C-TTTTTTCTTTTAATTTCA-CTCCATTTATTTTCTAATTT
65 TCTTTTTAATTTAATCCTTAA-ACCTTTTTTTCTTTTAATTCCACCT-CATTTATTTTCTAATTC
*
45481 TACAAATTAAGCCCCCGAACTC
128 TACAAATTAAGCCCCCAAACTC
*
45503 TTCAAAAATACGATTTCGACCTCGTTTTTCTATTTTTTA--ATTATTTTTTACGTAAAATTTAAT
1 TTCAAAAATACGATTTCGA-CTCGTTTTTCTATTTTTTATTATTA-TTTTTACCTAAAATTTAAT
* * *
45566 TTCCTTTTTAATTTAATCTTTAAACCTTTTTTTCTTTTAATTCCACCTCATTTATTTTTTGATTC
64 TT-CTTTTTAATTTAATCCTTAAACCTTTTTTTCTTTTAATTCCACCTCATTTATTTTCTAATTC
* *
45631 TACAAATTAGGCCTCCAAACTC
128 TACAAATTAAGCCCCCAAACTC
45653 TTCAAAAAT
1 TTCAAAAAT
45662 TTGTTTTTTG
Statistics
Matches: 136, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
147 4 0.03
148 30 0.22
149 41 0.30
150 59 0.43
151 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (149 bp):
TTCAAAAATACGATTTCGACTCGTTTTTCTATTTTTTATTATTATTTTTACCTAAAATTTAATTT
CTTTTTAATTTAATCCTTAAACCTTTTTTTCTTTTAATTCCACCTCATTTATTTTCTAATTCTAC
AAATTAAGCCCCCAAACTC
Done.