Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009790.1 Kokia drynarioides strain JFW-HI SEQ_124511, 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: 116462
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:1208 original size:23 final size:23
Alignment explanation
Indices: 1156--1278 Score: 76
Period size: 25 Copynumber: 5.2 Consensus size: 23
1146 ACACTAGCAC
*
1156 GCTCTCTGTTCAGCACTGTGTGT
1 GCTCTCTGTTCAGCACTGTCTGT
* *
1179 TCCCTCTGTTCAGCAC-GTCTCGT
1 GCTCTCTGTTCAGCACTGTCT-GT
* *
1202 GCTCTCTATTATTAGCACT-TCATGT
1 GCTCTCT-GT-TCAGCACTGTC-TGT
*
1227 GCTCTCTGTTATTAGCACT-TCATGT
1 GCTCTCTG-T-TCAGCACTGTC-TGT
1252 GCTCTCTGATT-AGCACT-TCGTGT
1 GCTCTCTG-TTCAGCACTGTC-TGT
1275 GCTC
1 GCTC
1279 AATACTTTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
22 3 0.04
23 36 0.43
24 2 0.02
25 42 0.50
26 1 0.01
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (23 bp):
GCTCTCTGTTCAGCACTGTCTGT
Found at i:1218 original size:25 final size:25
Alignment explanation
Indices: 1200--1278 Score: 117
Period size: 25 Copynumber: 3.2 Consensus size: 25
1190 AGCACGTCTC
1200 GTGCTCTCTATTATTAGCACTTCAT
1 GTGCTCTCTATTATTAGCACTTCAT
*
1225 GTGCTCTCTGTTATTAGCACTTCAT
1 GTGCTCTCTATTATTAGCACTTCAT
* *
1250 GTGCTCTC--TGATTAGCACTTCGT
1 GTGCTCTCTATTATTAGCACTTCAT
1273 GTGCTC
1 GTGCTC
1279 AATACTTTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
23 19 0.37
25 32 0.63
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (25 bp):
GTGCTCTCTATTATTAGCACTTCAT
Found at i:1331 original size:23 final size:23
Alignment explanation
Indices: 1281--1331 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1271 GTGTGCTCAA
*
1281 TACTTTGTGTACTCTCTATTTAG
1 TACTTTGTGTACTCTCTATTCAG
* * *
1304 CACTTTGTGTGCTCTCTGTTCAG
1 TACTTTGTGTACTCTCTATTCAG
1327 TACTT
1 TACTT
1332 CAGTACTCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (23 bp):
TACTTTGTGTACTCTCTATTCAG
Found at i:4105 original size:21 final size:20
Alignment explanation
Indices: 4081--4121 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4071 GAAAAGTATC
4081 TACAAAAAGAATCTCTAAGAT
1 TACAAAAA-AATCTCTAAGAT
**
4102 TACAATCAAATCTCTAAGAT
1 TACAAAAAAATCTCTAAGAT
4122 CATAAGGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (20 bp):
TACAAAAAAATCTCTAAGAT
Found at i:9092 original size:21 final size:20
Alignment explanation
Indices: 9068--9109 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9058 TGAAAAGTTT
9068 TTACAAAAAGAATCTCTAAGA
1 TTACAAAAA-AATCTCTAAGA
**
9089 TTACAATCAAATCTCTAAGA
1 TTACAAAAAAATCTCTAAGA
9109 T
1 T
9110 CATAAGGATC
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:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (20 bp):
TTACAAAAAAATCTCTAAGA
Found at i:26643 original size:18 final size:17
Alignment explanation
Indices: 26604--26651 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
26594 TTTTAGAATT
* *
26604 TTATAATTTTTTTAAAA
1 TTATAAATTTTATAAAA
*
26621 ATATAAATTTTATAAATA
1 TTATAAATTTTATAAA-A
26639 TTATAAATATTTA
1 TTATAAAT-TTTA
26652 GAATTTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 13 0.52
18 8 0.32
19 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAAATTTTATAAAA
Found at i:27072 original size:6 final size:6
Alignment explanation
Indices: 27063--27098 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
27053 ATTGAAAAGG
*
27063 AAAGAA AAAGAA AAAGAA AAAG-A AAAGAA AAGGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
27099 GGAAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:27082 original size:11 final size:11
Alignment explanation
Indices: 27057--27105 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
27047 TTTAATATTG
*
27057 AAAAGGAAAGA
1 AAAAGAAAAGA
27068 AAAAGAAAAAGA
1 AAAAG-AAAAGA
27080 AAAAGAAAAGA
1 AAAAGAAAAGA
* *
27091 AAAGGAAAGGA
1 AAAAGAAAAGA
27102 AAAA
1 AAAA
27106 AAGTCCCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 23 0.70
12 10 0.30
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAGA
Found at i:29088 original size:23 final size:20
Alignment explanation
Indices: 29021--29090 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 20
29011 TGTTATATAC
*
29021 TATAAAAATAATATATTTATT
1 TATAAAAA-AATATATTAATT
* *
29042 TATAAAAAAATATTATAAAGT
1 TATAAAAAAATA-TATTAATT
29063 TATGACAAAAAATTATATTAATT
1 TAT-A-AAAAAA-TATATTAATT
29086 TATAA
1 TATAA
29091 GAAGTGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
20 4 0.10
21 17 0.43
22 2 0.05
23 15 0.38
24 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (20 bp):
TATAAAAAAATATATTAATT
Found at i:29135 original size:14 final size:15
Alignment explanation
Indices: 29116--29153 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
29106 TTATCGGACA
29116 ATTTATAAA-ACTAT
1 ATTTATAAAGACTAT
*
29130 ATTTATAAAGATTAT
1 ATTTATAAAGACTAT
29145 ATGTTATAA
1 AT-TTATAA
29154 TTTTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 6 0.29
16 6 0.29
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (15 bp):
ATTTATAAAGACTAT
Found at i:42951 original size:29 final size:30
Alignment explanation
Indices: 42899--42998 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 30
42889 TAACCTTTAC
*
42899 AAAAGTGCTCAAATGAAAGTC-AAACATTTT-
1 AAAA-TGCTCAAAT-AAAGCCAAAACATTTTG
*
42929 AAAATGCTCAAATAAAGGCCAAAACTTTTTG
1 AAAATGCTCAAATAAA-GCCAAAACATTTTG
* * * * *
42960 AAAGTTCTCAAATAAGAGCTAAACCTTTTTG
1 AAAATGCTCAAATAA-AGCCAAAACATTTTG
*
42991 AAAGTGCT
1 AAAATGCT
42999 TTCAAATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.05
29 11 0.19
30 12 0.20
31 32 0.54
32 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (30 bp):
AAAATGCTCAAATAAAGCCAAAACATTTTG
Found at i:42973 original size:31 final size:31
Alignment explanation
Indices: 42935--42995 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
42925 TTTTAAAATG
42935 CTCAAATAA-AGGCCAAAACTTTTTGAAAGTT
1 CTCAAATAAGA-GCCAAAACTTTTTGAAAGTT
* *
42966 CTCAAATAAGAGCTAAACCTTTTTGAAAGT
1 CTCAAATAAGAGCCAAAACTTTTTGAAAGT
42996 GCTTTCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (31 bp):
CTCAAATAAGAGCCAAAACTTTTTGAAAGTT
Found at i:45808 original size:20 final size:20
Alignment explanation
Indices: 45772--45814 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
45762 AATTATAATG
45772 ATTTTTAAATTTTAAAA-TA
1 ATTTTTAAATTTTAAAATTA
*
45791 ATTTTTTAATTTTAAAAATTA
1 ATTTTTAAATTTT-AAAATTA
45812 ATT
1 ATT
45815 AAATGCTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 4 0.19
21 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTAAATTTTAAAATTA
Found at i:49184 original size:30 final size:30
Alignment explanation
Indices: 49148--49206 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
49138 AAAAGAAAAT
49148 GATAGATGAATTAGCTAAACAGTAAACACA
1 GATAGATGAATTAGCTAAACAGTAAACACA
49178 GATAGATGAATTAGCTAAACAGTAAACAC
1 GATAGATGAATTAGCTAAACAGTAAACAC
49207 CAATTATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (30 bp):
GATAGATGAATTAGCTAAACAGTAAACACA
Found at i:49919 original size:2 final size:2
Alignment explanation
Indices: 49908--49941 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
49898 GATCATGATG
49908 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49942 CAATTTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52841 original size:30 final size:30
Alignment explanation
Indices: 52781--52841 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
52771 TTTGGGGAAG
* *
52781 TAAAATTTTGAGGGAAAGTAAATAAGAAAA
1 TAAAATTTTGAGGGAAAATAAATAAAAAAA
*
52811 TAAAATTTTGGAGGGAAAAT-ATTAAAAAAA
1 TAAAATTTT-GAGGGAAAATAAATAAAAAAA
52841 T
1 T
52842 TTGGAGGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (30 bp):
TAAAATTTTGAGGGAAAATAAATAAAAAAA
Found at i:52934 original size:16 final size:16
Alignment explanation
Indices: 52886--52935 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
52876 GGGGGGGGAG
52886 GGGAGTAAAAGTTTTA
1 GGGAGTAAAAGTTTTA
* ***
52902 GGG-G-GAAAGTAAGA
1 GGGAGTAAAAGTTTTA
52916 GGGAGTAAAAGTTTTA
1 GGGAGTAAAAGTTTTA
52932 GGGA
1 GGGA
52936 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 4
0.67 0.22 0.11
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
16 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (16 bp):
GGGAGTAAAAGTTTTA
Found at i:53118 original size:21 final size:22
Alignment explanation
Indices: 53080--53126 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
53070 GGGAATGAGT
*
53080 AAAAGTTTTTGGGAAAAAATAA
1 AAAAGTTTTGGGGAAAAAATAA
* *
53102 AAAAG-TTTGGGGTAAAAATAT
1 AAAAGTTTTGGGGAAAAAATAA
53123 AAAA
1 AAAA
53127 TATTATAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (22 bp):
AAAAGTTTTGGGGAAAAAATAA
Found at i:64524 original size:29 final size:29
Alignment explanation
Indices: 64492--64552 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
64482 AAAATGAGAC
* *
64492 TTTTTGGA-TACCCGGGGGTAAAATGGTAA
1 TTTTTGGACT-CCCGAGGGCAAAATGGTAA
*
64521 -TTTTGGACTCTCGAGGGCAAAATGGTAA
1 TTTTTGGACTCCCGAGGGCAAAATGGTAA
64549 TTTT
1 TTTT
64553 AGGAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTTTGGACTCCCGAGGGCAAAATGGTAA
Found at i:64582 original size:58 final size:57
Alignment explanation
Indices: 64519--64775 Score: 191
Period size: 58 Copynumber: 4.4 Consensus size: 57
64509 GTAAAATGGT
* *
64519 AATTTTGGAC-TCTCGAGGGCAAAATGGTAATTTTAGGAAAATTTGGGGTTAAAAATGA
1 AATTTTGGACATC-CGAGGGTAAAATGGTAATTTTA-GAAAATTTGGGGTAAAAAATGA
* * * ** *
64577 AATTTTAGACATCCAAGGGTAAAATGGTAATTTTTAGAAAAATCAGGATAAAAAACT-A
1 AATTTTGGACATCCGAGGGTAAAATGGTAA-TTTTAGAAAATTTGGGGTAAAAAA-TGA
* * *
64635 AATTTTTGGACATCCGAGGGTAAAATGATAATTTT-GAAAGTTTTGGGGTCAAAAATGGA
1 AA-TTTTGGACATCCGAGGGTAAAATGGTAATTTTAGAAA-ATTTGGGGTAAAAAAT-GA
** * * * * * * *
64694 GTTTTTGGATATTCGGGGGT-AAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGA
1 AATTTTGGACATCCGAGGGTAAAATGGTAATTTTAGAAAATTT-GGGGTAAAAAAT-GA
* *
64752 ATTTTTGGA-AGTTCGAGGGTAAAA
1 AATTTTGGACA-TCCGAGGGTAAAA
64776 ATATAAGTTT
Statistics
Matches: 161, Mismatches: 27, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
57 21 0.13
58 103 0.64
59 37 0.23
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.32
Consensus pattern (57 bp):
AATTTTGGACATCCGAGGGTAAAATGGTAATTTTAGAAAATTTGGGGTAAAAAATGA
Found at i:64667 original size:29 final size:29
Alignment explanation
Indices: 64482--64669 Score: 77
Period size: 29 Copynumber: 6.5 Consensus size: 29
64472 ATCGGAGTTG
* * * * *
64482 AAAATGAGACTTTTTGGATACCCGGGGGT
1 AAAATGATAATTTTTGGACATCCGAGGGT
* *
64511 AAAATGGTAA-TTTTGGAC-TCTCGAGGGC
1 AAAATGATAATTTTTGGACATC-CGAGGGT
* * * **
64539 AAAATGGTAATTTTAGGAAAATTTG-GGGTT
1 AAAATGATAATTTTTGG-ACATCCGAGGG-T
* *
64569 AAAAATGA-AA-TTTTAGACATCCAAGGGT
1 -AAAATGATAATTTTTGGACATCCGAGGGT
* * * *
64597 AAAATGGTAATTTTTAGAAAAAT-C-AGGAT
1 AAAATGATAATTTTT-G-GACATCCGAGGGT
*
64626 AAAA-AACTAAATTTTTGGACATCCGAGGGT
1 AAAATGA-T-AATTTTTGGACATCCGAGGGT
64656 AAAATGATAATTTT
1 AAAATGATAATTTT
64670 GAAAGTTTTG
Statistics
Matches: 113, Mismatches: 30, Indels: 32
0.65 0.17 0.18
Matches are distributed among these distances:
27 7 0.06
28 31 0.27
29 43 0.38
30 21 0.19
31 11 0.10
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (29 bp):
AAAATGATAATTTTTGGACATCCGAGGGT
Found at i:64670 original size:28 final size:28
Alignment explanation
Indices: 64493--64670 Score: 71
Period size: 28 Copynumber: 6.2 Consensus size: 28
64483 AAATGAGACT
* * * *
64493 TTTTGGATACCCGGGGGTAAAATGGTAA
1 TTTTGGACATCCGAGGGTAAAATGATAA
* *
64521 TTTTGGAC-TCTCGAGGGCAAAATGGTAA
1 TTTTGGACATC-CGAGGGTAAAATGATAA
* **
64549 TTTTAGGAAAATTTG-GGGTTAAAAATGA-AA
1 TTTT-GG-ACATCCGAGGG-T-AAAATGATAA
* * *
64579 TTTTAGACATCCAAGGGTAAAATGGTAA
1 TTTTGGACATCCGAGGGTAAAATGATAA
* * * *
64607 TTTTTAGAAAAAT-C-AGGATAAAA-AACTAAA
1 -TTTT-G-GACATCCGAGGGTAAAATGA-T-AA
64637 TTTTTGGACATCCGAGGGTAAAATGATAA
1 -TTTTGGACATCCGAGGGTAAAATGATAA
64666 TTTTG
1 TTTTG
64671 AAAGTTTTGG
Statistics
Matches: 109, Mismatches: 25, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
27 7 0.06
28 40 0.37
29 26 0.24
30 25 0.23
31 11 0.10
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (28 bp):
TTTTGGACATCCGAGGGTAAAATGATAA
Found at i:64700 original size:30 final size:30
Alignment explanation
Indices: 64666--64777 Score: 94
Period size: 30 Copynumber: 3.8 Consensus size: 30
64656 AAAATGATAA
* *
64666 TTTTGAAAGTTTTGGGGTCAAAAATGGAGT
1 TTTTGAAAGTTTCGGGGTCAAAAATGGAAT
*
64696 TTTTG-GA-TATTCGGGGGT---AAATGGTAAT
1 TTTTGAAAGT-TTC-GGGGTCAAAAATGG-AAT
*
64724 TTTTGAAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTGAAAGTTTCGGGGTCAAAAATGGAAT
*
64754 TTTTGGAAG-TTCGAGGGT-AAAAAT
1 TTTTGAAAGTTTCG-GGGTCAAAAAT
64778 ATAAGTTTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 19
0.72 0.08 0.21
Matches are distributed among these distances:
27 6 0.09
28 12 0.18
29 17 0.26
30 25 0.38
31 6 0.09
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (30 bp):
TTTTGAAAGTTTCGGGGTCAAAAATGGAAT
Found at i:65823 original size:19 final size:19
Alignment explanation
Indices: 65780--65820 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
65770 TTATTTCTAA
65780 TATTATTAATAATACTATT
1 TATTATTAATAATACTATT
* *
65799 TATTATTATTAATGCT-TT
1 TATTATTAATAATACTATT
65817 TATT
1 TATT
65821 TATAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTATTAATAATACTATT
Found at i:67222 original size:206 final size:201
Alignment explanation
Indices: 66868--67448 Score: 781
Period size: 206 Copynumber: 2.9 Consensus size: 201
66858 CTTAGCCTTT
* *
66868 TTCTCAGTATCTCATCAA-GAAGATGACCGCATCACTTGCTTCAATCCGCTTCTTTGTATCTCAT
1 TTCTCAGTATCTCAT-AAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* ** * * *
66932 CAGGAAGATGAATTTGGTCCACTTCTTGGTATCTCATCAGGAAGTTAACCATTTTAATACTTCGA
65 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* *
66997 CCTA-TTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTC
130 CC-AGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGC----CTC
* * *
67061 TAATTTGGTCTTC
190 -AAGTTGGTATAC
* * *
67074 TTCTCAGTATCTCATAAGGAAGATGACCACATCGCTTATTTCAATCCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATAAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
*
67139 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGGAGCTAACCATTTTATTGCTTCGAC
66 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
* * * *
67204 CAGCTTCTCAATATCTCATCAGGAAGCTAGGATTCGAAGATTTGCTCCCATTGAGCCTCGAGTTG
131 CAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCCTCAAGTTG
67269 GTATAC
196 GTATAC
* * * *
67275 TTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATC
1 TTCTCAGTATCTCATAAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
* *
67340 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTTATTGCTTC-AC
66 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA-
* * * * *
67404 CCCGCTTCTCAGTATCTCATCAGGAAACTGGGGTTCAAAGATTTG
130 CCAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTG
67449 TTCGCATTGA
Statistics
Matches: 335, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
200 1 0.00
201 164 0.49
202 2 0.01
205 3 0.01
206 165 0.49
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (201 bp):
TTCTCAGTATCTCATAAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
CAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCCTCAAGTTG
GTATAC
Found at i:67369 original size:201 final size:200
Alignment explanation
Indices: 66868--67508 Score: 787
Period size: 201 Copynumber: 3.2 Consensus size: 200
66858 CTTAGCCTTT
* * *
66868 TTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGCTTCAATCCGCTTCTTTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
* ** * * *
66933 AGGAAGATGAATTTGGTCCACTTCTTGGTATCTCATCAGGAAGTTAACCATTTTAATACTTCGAC
66 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
* *
66998 CTA-TTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTCT
131 C-AGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAGC-----TC-
* * * *
67062 AATTTGGTCTTC
189 GAGTTGGTATAC
* * * *
67074 TTCTCAGTATCTCATAAGGAAGATGACCACATCGCTTATTTCAATCCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
*
67139 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGGAGCTAACCATTTTATTGCTTCGAC
66 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
* *
67204 CAGCTTCTCAATATCTCATCAGGAAGCTAGGATTCGAAGATTTGCTCCCATTGAGCCTCGAGTTG
131 CAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAG-CTCGAGTTG
67269 GTATAC
195 GTATAC
* * *
67275 TTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
* *
67340 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTTATTGCTTC-AC
66 AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA-
* * * * * * *
67404 CCCGCTTCTCAGTATCTCATCAGGAAACTGGGGTTCAAAGATTTGTTCGCA-T----T-GAGTTG
130 CCAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAGCTCGAGTTG
67463 GTATAC
195 GTATAC
* * * * *
67469 TTCTCTGTATCTCATTAGGAAGACGATCGCCTCAC-TGTTT
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTT
67509 GTGGATAATC
Statistics
Matches: 389, Mismatches: 43, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
193 5 0.01
194 44 0.11
195 1 0.00
200 2 0.01
201 168 0.43
202 2 0.01
205 1 0.00
206 165 0.42
207 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (200 bp):
TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATC
AGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
CAGCTTCTCAATATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACATTGAGCTCGAGTTGG
TATAC
Found at i:67664 original size:79 final size:79
Alignment explanation
Indices: 67571--67716 Score: 238
Period size: 79 Copynumber: 1.8 Consensus size: 79
67561 TCTGTCCCAA
* * * *
67571 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCCAAGCTTGGGGTAAAAGATCTAATGGCTT
1 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGACTT
67636 CAATCTGGCCCTAG
66 CAATCTGGCCCTAG
* *
67650 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCTAGGCTCGAGGTAAAAGATCAAATGACTT
1 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGACTT
67715 CA
66 CA
67717 TTGTAACTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (79 bp):
GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGACTT
CAATCTGGCCCTAG
Found at i:67682 original size:40 final size:39
Alignment explanation
Indices: 67571--67704 Score: 146
Period size: 39 Copynumber: 3.4 Consensus size: 39
67561 TCTGTCCCAA
* *
67571 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCCAA
1 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCTAG
* ** * * *
67610 GCTTGGGGTAAAAGATCTAATGGCT--TCAATCTGGCCCTAG
1 GCTCGGGGTAAAAGAT-TGGTTGATGAT-GATCT-GCCCTAG
67650 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCTAG
1 GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCTAG
*
67689 GCTCGAGGTAAAAGAT
1 GCTCGGGGTAAAAGAT
67705 CAAATGACTT
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
38 1 0.01
39 45 0.60
40 28 0.37
41 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (39 bp):
GCTCGGGGTAAAAGATTGGTTGATGATGATCTGCCCTAG
Found at i:68127 original size:48 final size:49
Alignment explanation
Indices: 67998--68307 Score: 234
Period size: 50 Copynumber: 6.3 Consensus size: 49
67988 CGACTTAAAC
* * * * *
67998 CTTTCCCTTCATGTCTTC-GTGGTACTGGATTCGTCGTTTGCAGCTTA-ACT
1 CTTTCCCTTGATGT-TTCTGTGGTACTAGATCCGCCG-TTGCGGCTTAGA-T
* * * *
68048 CTTTCCCTTTATGTCTCCGTGGTACTGGATCCGCCGTTGCGGCTTAGAT
1 CTTTCCCTTGATGTTTCTGTGGTACTAGATCCGCCGTTGCGGCTTAGAT
* * *
68097 TTTTCCCTTG-TGTTTTTGTGGTACTAGATCCACCGTTGCGGCTTAGAT
1 CTTTCCCTTGATGTTTCTGTGGTACTAGATCCGCCGTTGCGGCTTAGAT
* * * * ** *
68145 CTTTCCCTTGATGCTTCTGAGGTACAAGGTTTGCCGTTGCGACTTAGAT
1 CTTTCCCTTGATGTTTCTGTGGTACTAGATCCGCCGTTGCGGCTTAGAT
* * * * * * * * *
68194 ATTTCCCTTGATGTCTTCTGAGGTACTAGGTTCGCCATTACGACTTAAAC
1 CTTTCCCTTGATGT-TTCTGTGGTACTAGATCCGCCGTTGCGGCTTAGAT
* * * *
68244 CTTTCCTTCTG-TGTCTT-TGTGGCACTGGATCCGTCGTTGCGGTCTTAGAT
1 CTTTCCCT-TGATGT-TTCTGTGGTACTAGATCCGCCGTTGCGG-CTTAGAT
68294 CTTTCCCTTGATGT
1 CTTTCCCTTGATGT
68308 CTCATGGTGC
Statistics
Matches: 209, Mismatches: 44, Indels: 14
0.78 0.16 0.05
Matches are distributed among these distances:
48 42 0.20
49 79 0.38
50 86 0.41
51 2 0.01
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (49 bp):
CTTTCCCTTGATGTTTCTGTGGTACTAGATCCGCCGTTGCGGCTTAGAT
Found at i:68238 original size:50 final size:50
Alignment explanation
Indices: 67959--68309 Score: 190
Period size: 50 Copynumber: 7.1 Consensus size: 50
67949 CTTTTTCGTT
* * * * ** *
67959 ATGT-TTCTAAGGTAC-AGGGTTTGCCATTGCGACTTAAACCTTTCCCTTC
1 ATGTCTTCTGAGGTACTA-GGTTCGCCGTTGCGACTTAGATATTTCCCTTG
* * * *
68008 ATGTCTTC-GTGGTACT-GGATTCGTCGTTTGC-AGCTTA-ACTCTTTCCCTTT
1 ATGTCTTCTGAGGTACTAGG-TTCGCCG-TTGCGA-CTTAGA-TATTTCCCTTG
* * * * *
68058 ATGTC-TCCGTGGTACT-GGATCCGCCGTTGCGGCTTAGATTTTTCCCTTG
1 ATGTCTTCTGAGGTACTAGG-TTCGCCGTTGCGACTTAGATATTTCCCTTG
* * * * * * *
68107 -TGT-TTTTGTGGTACTAGATCCACCGTTGCGGCTTAGATCTTTCCCTTG
1 ATGTCTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAGATATTTCCCTTG
* *
68155 ATG-CTTCTGAGGTACAAGGTTTGCCGTTGCGACTTAGATATTTCCCTTG
1 ATGTCTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAGATATTTCCCTTG
* * * ** *
68204 ATGTCTTCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCTTCTG
1 ATGTCTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAGATATTTCCCT-TG
* * * * * *
68255 -TGTCTT-TGTGGCACT-GGATCCGTCGTTGCGGTCTTAGATCTTTCCCTTG
1 ATGTCTTCTGAGGTACTAGG-TTCGCCGTTGC-GACTTAGATATTTCCCTTG
68304 ATGTCT
1 ATGTCT
68310 CATGGTGCTG
Statistics
Matches: 240, Mismatches: 44, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
48 44 0.18
49 92 0.38
50 102 0.43
51 2 0.01
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (50 bp):
ATGTCTTCTGAGGTACTAGGTTCGCCGTTGCGACTTAGATATTTCCCTTG
Found at i:69543 original size:7 final size:6
Alignment explanation
Indices: 69526--69589 Score: 69
Period size: 7 Copynumber: 10.3 Consensus size: 6
69516 CGACCTCTCC
*
69526 TTTTCT TTTTCGT TTTTCT ATTTTCT TTTTCCT TTTTCCT TTTTC- CTTT-T
1 TTTTCT TTTTC-T TTTTCT -TTTTCT TTTT-CT TTTT-CT TTTTCT TTTTCT
69576 TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TT
69590 CTTCAATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
5 6 0.12
6 20 0.39
7 25 0.49
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:69551 original size:20 final size:20
Alignment explanation
Indices: 69526--69576 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
69516 CGACCTCTCC
*
69526 TTTTCTTTTTCGTTTTT-CT
1 TTTTCTTTTTCCTTTTTCCT
69545 ATTTTCTTTTTCCTTTTTCCT
1 -TTTTCTTTTTCCTTTTTCCT
69566 TTTTCCTTTTT
1 TTTT-CTTTTT
69577 TTTCTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTTCCTTTTTCCT
Found at i:75417 original size:59 final size:59
Alignment explanation
Indices: 75354--75644 Score: 243
Period size: 59 Copynumber: 4.9 Consensus size: 59
75344 AAAATCACGA
*
75354 TAAAAAACGGAATTTTTGGACATTAGGGGGT-AAAATGATAATTTT-AAAAGTTTCGAGG
1 TAAAAAATGGAATTTTTGGACATTAGGGGGTAAAAAT-ATAATTTTCAAAAGTTTCGAGG
* * ** * * *** * *
75412 TTAAAAATGGAATTTTTAGACATCCGAGGGT-AAAATGGTAATTTTTTGGATGTTTTG-GAG
1 TAAAAAATGGAATTTTTGGACATTAGGGGGTAAAAAT-ATAA-TTTTCAAAAGTTTCGAG-G
* *
75472 TCAAAAATGGAATTTTTGGA-AGTTCA-GAGGTAAAAATATAATTTTCAAAAGTTTCGAGG
1 TAAAAAATGGAATTTTTGGACA-TT-AGGGGGTAAAAATATAATTTTCAAAAGTTTCGAGG
* * * *
75531 TCAAAAATGGAATCTTTGGAAATTTGGGGGTAAAAATATAATTTTCAAAAGTTTCGAGG
1 TAAAAAATGGAATTTTTGGACATTAGGGGGTAAAAATATAATTTTCAAAAGTTTCGAGG
* ** * * * * *
75590 TTAAAAATAAAATCTTTGGAAATTCGGGGGTAAAAAAATAATTTTCGAATAGTTT
1 TAAAAAATGGAATTTTTGGACATTAGGGGGTAAAAATATAATTTTC-AAAAGTTT
75645 AGAGACCTTC
Statistics
Matches: 191, Mismatches: 32, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
58 34 0.18
59 111 0.58
60 41 0.21
61 5 0.03
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.34
Consensus pattern (59 bp):
TAAAAAATGGAATTTTTGGACATTAGGGGGTAAAAATATAATTTTCAAAAGTTTCGAGG
Found at i:75425 original size:29 final size:29
Alignment explanation
Indices: 75393--75597 Score: 89
Period size: 29 Copynumber: 6.9 Consensus size: 29
75383 GTAAAATGAT
75393 AATTTTAAAAGTTTCGAGGTTAAAAATGG
1 AATTTTAAAAGTTTCGAGGTTAAAAATGG
* * ** * *
75422 AATTTTTAGACATCCGAGGGT-AAAATGG
1 AATTTTAAAAGTTTCGAGGTTAAAAATGG
** * * *
75450 TAATTTTTTGGATGTTTTG-GAGTCAAAAATGG
1 -AA--TTTTAAAAGTTTCGAG-GTTAAAAATGG
** **
75482 AATTTTTGGAAG-TTCAGAGG-TAAAAATAT
1 AA-TTTTAAAAGTTTC-GAGGTTAAAAATGG
*
75511 AATTTTCAAAAGTTTCGAGGTCAAAAATGG
1 AATTTT-AAAAGTTTCGAGGTTAAAAATGG
* * * **
75541 AATCTTTGGAAA-TTT-GGGGGTAAAAATAT
1 AAT-TTT-AAAAGTTTCGAGGTTAAAAATGG
75570 AATTTTCAAAAGTTTCGAGGTTAAAAAT
1 AATTTT-AAAAGTTTCGAGGTTAAAAAT
75598 AAAATCTTTG
Statistics
Matches: 126, Mismatches: 37, Indels: 25
0.67 0.20 0.13
Matches are distributed among these distances:
28 17 0.13
29 49 0.39
30 37 0.29
31 16 0.13
32 7 0.06
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
AATTTTAAAAGTTTCGAGGTTAAAAATGG
Found at i:75429 original size:30 final size:30
Alignment explanation
Indices: 75395--75597 Score: 107
Period size: 30 Copynumber: 6.8 Consensus size: 30
75385 AAAATGATAA
75395 TTTTAAAAGTTTCGAGGTTAAAAATGGAAT
1 TTTTAAAAGTTTCGAGGTTAAAAATGGAAT
* * *
75425 TTTTAGACA--TCCGAGGGT-AAAATGGTAATT
1 TTTTA-AAAGTTTCGAGGTTAAAAATGG-AA-T
** * * *
75455 TTTTGGATGTTTTG-GAGTCAAAAATGGAAT
1 TTTTAAAAGTTTCGAG-GTTAAAAATGGAAT
** **
75485 TTTTGGAAG-TTCAGAGG-TAAAAATATAAT
1 TTTTAAAAGTTTC-GAGGTTAAAAATGGAAT
* *
75514 TTTCAAAAGTTTCGAGGTCAAAAATGGAAT
1 TTTTAAAAGTTTCGAGGTTAAAAATGGAAT
** * * **
75544 CTTTGGAAA-TTT-GGGGGTAAAAATATAAT
1 -TTTTAAAAGTTTCGAGGTTAAAAATGGAAT
*
75573 TTTCAAAAGTTTCGAGGTTAAAAAT
1 TTTTAAAAGTTTCGAGGTTAAAAAT
75598 AAAATCTTTG
Statistics
Matches: 126, Mismatches: 33, Indels: 28
0.67 0.18 0.15
Matches are distributed among these distances:
28 13 0.10
29 45 0.36
30 47 0.37
31 14 0.11
32 7 0.06
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (30 bp):
TTTTAAAAGTTTCGAGGTTAAAAATGGAAT
Found at i:75573 original size:119 final size:118
Alignment explanation
Indices: 75356--75575 Score: 277
Period size: 119 Copynumber: 1.9 Consensus size: 118
75346 AATCACGATA
* *
75356 AAAAACGGAATTTTTGGACATTAGGGGGTAAAATGATAATTTTAAAAGTTTCGAGGTTAAAAATG
1 AAAAACGGAATTTTTGGACATTAGGAGGTAAAATGATAATTTTAAAAGTTTCGAGGTCAAAAATG
* * *
75421 GAATTTTTAGACATCCGAGGGTAAAATGGTAATTTTTTGGATGTTTTGGAGTC
66 GAATCTTTAGAAATCCGAGGGTAAAATGATAATTTTTTGGATGTTTTGGAGTC
*
75474 AAAAATGGAATTTTTGGA-AGTTCA-GAGGTAAAAAT-ATAATTTTCAAAAGTTTCGAGGTCAAA
1 AAAAACGGAATTTTTGGACA-TT-AGGAGGT-AAAATGATAATTTT-AAAAGTTTCGAGGTCAAA
* ** *
75536 AATGGAATCTTTGGAAATTTGGGGGTAAAAAT-ATAATTTT
62 AATGGAATCTTTAGAAATCCGAGGGT-AAAATGATAATTTT
75576 CAAAAGTTTC
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
117 1 0.01
118 31 0.36
119 50 0.57
120 5 0.06
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (118 bp):
AAAAACGGAATTTTTGGACATTAGGAGGTAAAATGATAATTTTAAAAGTTTCGAGGTCAAAAATG
GAATCTTTAGAAATCCGAGGGTAAAATGATAATTTTTTGGATGTTTTGGAGTC
Found at i:75598 original size:30 final size:30
Alignment explanation
Indices: 75498--75598 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
75488 TGGAAGTTCA
75498 GAGG-TAAAAATATAATTTTCAAAAGTTTC
1 GAGGTTAAAAATATAATTTTCAAAAGTTTC
* ** **
75527 GAGGTCAAAAATGGAATCTTTGGAAA-TTT-
1 GAGGTTAAAAATATAAT-TTTCAAAAGTTTC
* *
75556 GGGGGTAAAAATATAATTTTCAAAAGTTTC
1 GAGGTTAAAAATATAATTTTCAAAAGTTTC
75586 GAGGTTAAAAATA
1 GAGGTTAAAAATA
75599 AAATCTTTGG
Statistics
Matches: 54, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
28 6 0.11
29 19 0.35
30 23 0.43
31 6 0.11
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.32
Consensus pattern (30 bp):
GAGGTTAAAAATATAATTTTCAAAAGTTTC
Found at i:75615 original size:29 final size:29
Alignment explanation
Indices: 75524--75625 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 29
75514 TTTCAAAAGT
**
75524 TTCGA-GGTCAAAAATGGAATCTTTGGAAA
1 TTCGAGGGT-AAAAATAAAATCTTTGGAAA
* * * **
75553 TTTGGGGGTAAAAATATAAT-TTTCAAAA
1 TTCGAGGGTAAAAATAAAATCTTTGGAAA
*
75581 GTTTCGAGGTTAAAAATAAAATCTTTGGAAA
1 --TTCGAGGGTAAAAATAAAATCTTTGGAAA
*
75612 TTCGGGGGTAAAAA
1 TTCGAGGGTAAAAA
75626 AATAATTTTC
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
28 6 0.11
29 24 0.44
30 19 0.35
31 6 0.11
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (29 bp):
TTCGAGGGTAAAAATAAAATCTTTGGAAA
Found at i:76958 original size:64 final size:64
Alignment explanation
Indices: 76885--77015 Score: 262
Period size: 64 Copynumber: 2.0 Consensus size: 64
76875 ATAAGTAAAG
76885 AATGAATAATAAATGATGACAGAGAGATGGTTGATATATGTTAATGCATATTAATGTATGTTAA
1 AATGAATAATAAATGATGACAGAGAGATGGTTGATATATGTTAATGCATATTAATGTATGTTAA
76949 AATGAATAATAAATGATGACAGAGAGATGGTTGATATATGTTAATGCATATTAATGTATGTTAA
1 AATGAATAATAAATGATGACAGAGAGATGGTTGATATATGTTAATGCATATTAATGTATGTTAA
77013 AAT
1 AAT
77016 TCAAAGCATT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (64 bp):
AATGAATAATAAATGATGACAGAGAGATGGTTGATATATGTTAATGCATATTAATGTATGTTAA
Found at i:77866 original size:55 final size:55
Alignment explanation
Indices: 77807--77937 Score: 160
Period size: 54 Copynumber: 2.4 Consensus size: 55
77797 CCATTGGATG
**
77807 AAAAAAATATTTTTAAATTTGAAAAATATGGGGTA-GATCATTGGGTGACAAACA-T
1 AAAAAAATATTTTTAAATTTGAAAAA-ATGGGGTATG-TCATTAAGTGACAAACACT
* * * *
77862 AAAAAAATATTTTTAAAATTGGAAAAGTGGTGTATGTCATTAAGTGACAAACACT
1 AAAAAAATATTTTTAAATTTGAAAAAATGGGGTATGTCATTAAGTGACAAACACT
*
77917 -CAAAAATATTTTTAAATTTGA
1 AAAAAAATATTTTTAAATTTGA
77938 GGAATGTTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
54 39 0.60
55 26 0.40
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (55 bp):
AAAAAAATATTTTTAAATTTGAAAAAATGGGGTATGTCATTAAGTGACAAACACT
Found at i:77969 original size:55 final size:55
Alignment explanation
Indices: 77809--77986 Score: 182
Period size: 55 Copynumber: 3.2 Consensus size: 55
77799 ATTGGATGAA
* * * *
77809 AAAAATATTTTTAAATTTGAAAAATATGGGGT-AGATCATTGGGTGACAAACA-TAA
1 AAAAATATTTTTAAATTTGAGAAATGTGGTGTAAG-TCATTGGGTGACAAACACT-C
* * * **
77864 AAAAATATTTTTAAAATTG-GAAAAGTGGTGTATGTCATTAAGTGACAAACACTC
1 AAAAATATTTTTAAATTTGAGAAATGTGGTGTAAGTCATTGGGTGACAAACACTC
* * **
77918 AAAAATATTTTTAAATTTGAGGAATGTTGTGTAAGTCATTGGGTGGGAAACACCTC
1 AAAAATATTTTTAAATTTGAGAAATGTGGTGTAAGTCATTGGGTGACAAACA-CTC
77974 AAAAAATATTTTT
1 -AAAAATATTTTT
77987 GGAACATAAA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
54 41 0.41
55 44 0.44
56 3 0.03
57 12 0.12
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (55 bp):
AAAAATATTTTTAAATTTGAGAAATGTGGTGTAAGTCATTGGGTGACAAACACTC
Found at i:78375 original size:26 final size:26
Alignment explanation
Indices: 78322--78384 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
78312 TTTTAGATCG
*
78322 TTATGTTTTAATTATAATTTTTTAAA
1 TTATGTTTTAATTATAATATTTTAAA
78348 TTATGTTTTAATTATTTAA-ATTTT-AA
1 TTATGTTTTAATTA--TAATATTTTAAA
*
78374 TTATTTTTTAA
1 TTATGTTTTAA
78385 AATTTTGGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 26 0.79
27 4 0.12
28 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (26 bp):
TTATGTTTTAATTATAATATTTTAAA
Found at i:78539 original size:57 final size:57
Alignment explanation
Indices: 78417--78526 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
78407 CCCTTGGATG
* * *
78417 AAAAAAATATTTTTAAATCTGAAAAATGTGGTGTAAATCATTGGGTGATAAACATAAA
1 AAAAAAATATTTTAAAATCTGAAAAATGTGGTGT-AATCATTAGGTGACAAACATAAA
78475 AAAAAAATACTTTTAAAAT-TGAAAAA-GTGGTGT-ATGCTATTAGGTGACAAAC
1 AAAAAAATA-TTTTAAAATCTGAAAAATGTGGTGTAAT-C-ATTAGGTGACAAAC
78527 TTTTAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
55 2 0.04
56 1 0.02
57 19 0.41
58 16 0.35
59 8 0.17
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.30
Consensus pattern (57 bp):
AAAAAAATATTTTAAAATCTGAAAAATGTGGTGTAATCATTAGGTGACAAACATAAA
Found at i:82050 original size:17 final size:19
Alignment explanation
Indices: 82006--82050 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
81996 TAAAGTCCTT
82006 TCATAATATCCAAATACAA
1 TCATAATATCCAAATACAA
*
82025 ACA-ATATAT-CAAATAC-A
1 TCATA-ATATCCAAATACAA
82042 TCATAATAT
1 TCATAATAT
82051 GCTTATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (19 bp):
TCATAATATCCAAATACAA
Found at i:90907 original size:36 final size:36
Alignment explanation
Indices: 90860--90928 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
90850 TCAGTTTAAC
* * *
90860 TCTTGCAAAGTGAGATTTTTTGATAAATATTCTAAT
1 TCTTGCAAAGTGAAATTTCTCGATAAATATTCTAAT
90896 TCTTGCAAAGTGAAATTTCTCGATAAATATTCT
1 TCTTGCAAAGTGAAATTTCTCGATAAATATTCT
90929 CTAAGACGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (36 bp):
TCTTGCAAAGTGAAATTTCTCGATAAATATTCTAAT
Found at i:92923 original size:11 final size:11
Alignment explanation
Indices: 92907--92949 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
92897 AAAAAAAATG
92907 TTGTTTTTTTA
1 TTGTTTTTTTA
* *
92918 TTGTTTTGTTG
1 TTGTTTTTTTA
* *
92929 TTATTTTCTTA
1 TTGTTTTTTTA
92940 TTGTTTTTTT
1 TTGTTTTTTT
92950 TCACTATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.07, C:0.02, G:0.12, T:0.79
Consensus pattern (11 bp):
TTGTTTTTTTA
Found at i:92935 original size:22 final size:22
Alignment explanation
Indices: 92905--92946 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
92895 AAAAAAAAAA
* *
92905 TGTTGTTTTTTTATTGTTTTGT
1 TGTTATTTTCTTATTGTTTTGT
92927 TGTTATTTTCTTATTGTTTT
1 TGTTATTTTCTTATTGTTTT
92947 TTTTCACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.02, G:0.14, T:0.76
Consensus pattern (22 bp):
TGTTATTTTCTTATTGTTTTGT
Found at i:109138 original size:2 final size:2
Alignment explanation
Indices: 109131--109158 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109121 TATAAAACAT
109131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
109159 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109163 original size:2 final size:2
Alignment explanation
Indices: 109158--109188 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
109148 ATATATATAT
109158 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
109189 AAGAAAGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:110981 original size:12 final size:13
Alignment explanation
Indices: 110957--110986 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
110947 ATTTTTAAAT
110957 AATTTTATTTTTA
1 AATTTTATTTTTA
110970 AATTTT-TTTTTA
1 AATTTTATTTTTA
110982 AATTT
1 AATTT
110987 ACAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
AATTTTATTTTTA
Found at i:112288 original size:29 final size:29
Alignment explanation
Indices: 112246--112303 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
112236 ATTACGTGGT
112246 TGTTTTGATTGAAGAATTAAAAGATTTGA
1 TGTTTTGATTGAAGAATTAAAAGATTTGA
112275 TGTTTTGATTGAAGAATTAAAAGATTTGA
1 TGTTTTGATTGAAGAATTAAAAGATTTGA
112304 CTCAAATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (29 bp):
TGTTTTGATTGAAGAATTAAAAGATTTGA
Done.