Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013389.1 Kokia drynarioides strain JFW-HI SEQ_128412, 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: 189382
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:13902 original size:12 final size:12
Alignment explanation
Indices: 13885--13925 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
13875 TAGGTTCTTT
13885 TTCTTCTTTCTC
1 TTCTTCTTTCTC
13897 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
13909 TTCTTC-TTCTTC
1 TTCTTCTTTC-TC
13921 TTCTT
1 TTCTT
13926 GATCCTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.12
11 1 0.04
12 17 0.65
13 5 0.19
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:22809 original size:29 final size:29
Alignment explanation
Indices: 22767--22827 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
22757 TAAGTCGGGA
*
22767 TTAAGTAGAGAGTTGTTGTTGGTAAGAAC
1 TTAAGTAGAGAGTTGCTGTTGGTAAGAAC
22796 TTAAGTAGAGAGTTGCTGTTGGTAAGAAC
1 TTAAGTAGAGAGTTGCTGTTGGTAAGAAC
22825 TTA
1 TTA
22828 GAGGGACTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (29 bp):
TTAAGTAGAGAGTTGCTGTTGGTAAGAAC
Found at i:38775 original size:21 final size:21
Alignment explanation
Indices: 38746--38800 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
38736 CCTTGTACTT
38746 CTACCGAAACATGCAAGAGTA
1 CTACCGAAACATGCAAGAGTA
* *
38767 CTACTGAAACATGCAATAGTA
1 CTACCGAAACATGCAAGAGTA
38788 CTACCGAAACATG
1 CTACCGAAACATG
38801 TATGCAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (21 bp):
CTACCGAAACATGCAAGAGTA
Found at i:56934 original size:72 final size:73
Alignment explanation
Indices: 56825--56970 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 73
56815 CAAGCTGCTG
56825 AGGACTCGCAACATAAAGCCTACTATCTTTTTCGTTTCACTTTCTCGATCATCTTCAATTCCAGA
1 AGGACTCGCAACATAAAGCCTACTATCTTTTTCGTTTCACTTTCTCGATCATCTTCAATTCCAGA
56890 -GCTGCCA
66 TGCTGCCA
56897 AGGACTCGCAACATAAAGCCTACTATCTTTTTCGTTTCACTTTCTCGATCATCTTCAATTCCAGA
1 AGGACTCGCAACATAAAGCCTACTATCTTTTTCGTTTCACTTTCTCGATCATCTTCAATTCCAGA
*
56962 TGCTTCCA
66 TGCTGCCA
56970 A
1 A
56971 TTTGCTGAAC
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 65 0.90
73 7 0.10
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.34
Consensus pattern (73 bp):
AGGACTCGCAACATAAAGCCTACTATCTTTTTCGTTTCACTTTCTCGATCATCTTCAATTCCAGA
TGCTGCCA
Found at i:62006 original size:21 final size:21
Alignment explanation
Indices: 61976--62015 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61966 TTTCCCTCCT
61976 TCTTC-CTTTTCTACTTCCTTC
1 TCTTCTCTTTTCT-CTTCCTTC
*
61997 TCTTCTTTTTTCTCTTCCT
1 TCTTCTCTTTTCTCTTCCT
62016 CAATATCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTTCTCTTTTCTCTTCCTTC
Found at i:80275 original size:27 final size:26
Alignment explanation
Indices: 80239--80336 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 26
80229 ATATGTATTT
*
80239 TTTATATTTTATA-TTATTAAATATA
1 TTTATATTTTTTATTTATTAAATATA
** *
80264 TTTATATTTTTTTATAAATTCAATTATA
1 TTTATA-TTTTTTATTTATT-AAATATA
*
80292 TTCA-ATTTTTTATTT-TT-AATATA
1 TTTATATTTTTTATTTATTAAATATA
* **
80315 ATTAT-TTTTCAATTTATTAAAT
1 TTTATATTTTTTATTTATTAAAT
80337 TTTAGTACCC
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
23 15 0.27
24 2 0.04
25 11 0.20
26 14 0.25
27 4 0.07
28 9 0.16
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATATTTTTTATTTATTAAATATA
Found at i:80333 original size:15 final size:15
Alignment explanation
Indices: 80292--80333 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
80282 TTCAATTATA
*
80292 TTCAATTTTTTATTT
1 TTCAATTTATTATTT
*
80307 TT-AATATAATTATTT
1 TTCAAT-TTATTATTT
80322 TTCAATTTATTA
1 TTCAATTTATTA
80334 AATTTTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.14
15 16 0.73
16 3 0.14
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TTCAATTTATTATTT
Found at i:88922 original size:34 final size:34
Alignment explanation
Indices: 88877--89029 Score: 171
Period size: 34 Copynumber: 4.5 Consensus size: 34
88867 GTTATCGTGT
* * * *
88877 TTTGGTATGTTGGATAGAATAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGATTAGCTCATACGAGCA
* * * *
88911 CTTGGTGTGTTGGTTGGACTAGCTCATACGAGTA
1 TTTGGTGTGTTGGATGGATTAGCTCATACGAGCA
* *
88945 TTTGGTGTGCTAGATGGATTAGCTCATACGAGCA
1 TTTGGTGTGTTGGATGGATTAGCTCATACGAGCA
* * * * *
88979 TTTGGCGTGCTGGATGGATTGGCTTATATGAGCA
1 TTTGGTGTGTTGGATGGATTAGCTCATACGAGCA
89013 TTTGGTGTGTTGGATGG
1 TTTGGTGTGTTGGATGG
89030 TTAACCGTGT
Statistics
Matches: 99, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 99 1.00
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.36
Consensus pattern (34 bp):
TTTGGTGTGTTGGATGGATTAGCTCATACGAGCA
Found at i:91437 original size:2 final size:2
Alignment explanation
Indices: 91432--91460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
91422 TCTCATTTGG
91432 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
91461 GTTGTAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92176 original size:24 final size:24
Alignment explanation
Indices: 92148--92197 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
92138 AACTATATGA
92148 ACGTTATAAAAACATTAGTTATAT
1 ACGTTATAAAAACATTAGTTATAT
92172 ACGTTATAAAAACATTAGTTATAT
1 ACGTTATAAAAACATTAGTTATAT
92196 AC
1 AC
92198 ATAATACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (24 bp):
ACGTTATAAAAACATTAGTTATAT
Found at i:92210 original size:7 final size:7
Alignment explanation
Indices: 92200--92224 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
92190 TTATATACAT
92200 AATACTA
1 AATACTA
92207 AATACTA
1 AATACTA
92214 AATACTA
1 AATACTA
92221 AATA
1 AATA
92225 TGAAATCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:93206 original size:18 final size:21
Alignment explanation
Indices: 93170--93211 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 21
93160 ATTCACATAA
*
93170 AAATTATAACAAAATTTAATT
1 AAATTATAACAAAATTTAAAT
93191 AAATTAT-A-AAAA-TTAAAT
1 AAATTATAACAAAATTTAAAT
93209 AAA
1 AAA
93212 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 4 0.20
20 1 0.05
21 7 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTATAACAAAATTTAAAT
Found at i:105043 original size:28 final size:27
Alignment explanation
Indices: 105000--105059 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
104990 GCTGTTGTCG
*
105000 AGCCAGATGCCATGCCTATTGTAGCCA
1 AGCCAGACGCCATGCCTATTGTAGCCA
* *
105027 AGCCAGACGCCCATGCCTATTGTTGCCG
1 AGCCAGACG-CCATGCCTATTGTAGCCA
105055 AGCCA
1 AGCCA
105060 TGTTTGCTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.28
28 21 0.72
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.20
Consensus pattern (27 bp):
AGCCAGACGCCATGCCTATTGTAGCCA
Found at i:110161 original size:40 final size:40
Alignment explanation
Indices: 110058--110149 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 40
110048 AACTCAACCC
110058 ATCTACCTGTCGTAAATGCAGAGACTGAATAAAAATATAT
1 ATCTACCTGTCGTAAATGCAGAGACTGAATAAAAATATAT
* * *
110098 -T-TTCCTATCATAAATGCAGAGACTGAATAAAAATATAT
1 ATCTACCTGTCGTAAATGCAGAGACTGAATAAAAATATAT
110136 ATCTACCTGTCGTA
1 ATCTACCTGTCGTA
110150 GATGTAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
38 34 0.77
39 2 0.05
40 8 0.18
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (40 bp):
ATCTACCTGTCGTAAATGCAGAGACTGAATAAAAATATAT
Found at i:113005 original size:21 final size:21
Alignment explanation
Indices: 112981--113030 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
112971 ATACTTGTAT
*
112981 CGGTAGAACCTCCATAACTAC
1 CGGTAGAACCTCCACAACTAC
*
113002 CGGTAGAACCTCTACAACTAC
1 CGGTAGAACCTCCACAACTAC
*
113023 CGGCAGAA
1 CGGTAGAA
113031 AATTGAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (21 bp):
CGGTAGAACCTCCACAACTAC
Found at i:118292 original size:14 final size:16
Alignment explanation
Indices: 118273--118306 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
118263 GCAAATATAA
118273 TTTTTTCT-TCTT-TT
1 TTTTTTCTCTCTTGTT
118287 TTTTTTCTCTCTTGTT
1 TTTTTTCTCTCTTGTT
118303 TTTT
1 TTTT
118307 CAAGTGACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 4 0.22
16 6 0.33
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTTCTCTCTTGTT
Found at i:121482 original size:6 final size:6
Alignment explanation
Indices: 121473--121564 Score: 59
Period size: 6 Copynumber: 15.2 Consensus size: 6
121463 AGAAAAAATG
*
121473 AGAAAA AG--AA AGAAAA AGAAAAA ATGAGAAA A-AGAA AGAAAA AGAAAAA
1 AGAAAA AGAAAA AGAAAA AG-AAAA A-GA-AAA AGAAAA AGAAAA AG-AAAA
* * *
121522 ATGTGAAA AG-GAA AGAAAA AGAAAG AG-AAA AGAAAA AGAAAA A
1 A-G-AAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA A
121565 AATTATGTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
4 4 0.06
5 11 0.16
6 31 0.46
7 12 0.18
8 10 0.15
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:121495 original size:26 final size:26
Alignment explanation
Indices: 121459--121566 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
121449 TTAGTCACTT
121459 AAAAAGAAAAAATGAGAAAAAGAAAG
1 AAAAAGAAAAAATGAGAAAAAGAAAG
121485 AAAAAGAAAAAATGAGAAAAAGAAAG
1 AAAAAGAAAAAATGAGAAAAAGAAAG
* *
121511 AAAAAGAAAAAATGTGAAAAGGAAAG
1 AAAAAGAAAAAATGAGAAAAAGAAAG
*
121537 AAAAAGAAAGAGAA-AAGAAAAAGAAA-
1 AAAAAGAAA-A-AATGAGAAAAAGAAAG
121563 AAAA
1 AAAA
121567 TTATGTTTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
26 63 0.84
27 10 0.13
28 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (26 bp):
AAAAAGAAAAAATGAGAAAAAGAAAG
Found at i:121518 original size:16 final size:16
Alignment explanation
Indices: 121459--121564 Score: 83
Period size: 16 Copynumber: 6.3 Consensus size: 16
121449 TTAGTCACTT
*
121459 AAAAAGAAA-AAATGAG
1 AAAAAGAAAGAAA-AAG
121475 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
121491 AAAAA-ATGAGAAAAAG
1 AAAAAGA-AAGAAAAAG
121507 AAAGAA-AAAGAAAAAATGTG
1 AAA-AAGAAAG-AAAAA---G
*
121527 AAAAGGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
121543 AAAGAGAAAAGAAAAAG
1 AAAAAG-AAAGAAAAAG
121560 AAAAA
1 AAAAA
121565 AATTATGTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.01
16 34 0.46
17 25 0.34
19 6 0.08
20 8 0.11
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:121539 original size:10 final size:10
Alignment explanation
Indices: 121473--121556 Score: 67
Period size: 10 Copynumber: 9.1 Consensus size: 10
121463 AGAAAAAATG
121473 AGAAAAAGAA
1 AGAAAAAGAA
121483 AGAAAAAG-A
1 AGAAAAAGAA
*
121492 A-AAAATG--
1 AGAAAAAGAA
121499 AGAAAAAGAA
1 AGAAAAAGAA
121509 AGAAAAAG-A
1 AGAAAAAGAA
*
121518 A-AAAATG--
1 AGAAAAAGAA
* *
121525 TGAAAAGGAA
1 AGAAAAAGAA
121535 AGAAAAAGAA
1 AGAAAAAGAA
121545 AGAGAAAAGAA
1 AGA-AAAAGAA
121556 A
1 A
121557 AAGAAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
7 1 0.02
8 20 0.33
9 4 0.07
10 27 0.45
11 8 0.13
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:129523 original size:31 final size:32
Alignment explanation
Indices: 129485--129580 Score: 117
Period size: 31 Copynumber: 3.1 Consensus size: 32
129475 ATAAATTATT
* * *
129485 TTATTTATAGT-TATTATTAATATTATACAGA
1 TTATTTATAGTGCATTATAAATATTATACACA
*
129516 TTATTTAT-GTGCATTATAAATATTGTACACA
1 TTATTTATAGTGCATTATAAATATTATACACA
* *
129547 TTATTTATA-CGCATTATAAATATTCTACACA
1 TTATTTATAGTGCATTATAAATATTATACACA
129578 TTA
1 TTA
129581 ATAAATTGCC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.04
31 55 0.96
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (32 bp):
TTATTTATAGTGCATTATAAATATTATACACA
Found at i:132913 original size:21 final size:21
Alignment explanation
Indices: 132887--132928 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
132877 TTCCATAAAG
132887 GAAAACTAAACTAAATCCTAA
1 GAAAACTAAACTAAATCCTAA
132908 GAAAACTAAACTAAATCCTAA
1 GAAAACTAAACTAAATCCTAA
132929 AATTCAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.19, G:0.05, T:0.19
Consensus pattern (21 bp):
GAAAACTAAACTAAATCCTAA
Found at i:133641 original size:25 final size:26
Alignment explanation
Indices: 133608--133662 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
133598 ACTTTTCAAA
*
133608 TTTT-TTCTTACTCATGAATT-TTTC
1 TTTTGTTCTTACTCATCAATTCTTTC
*
133632 TTTTGTTCTTACTCATCTATTCTTTC
1 TTTTGTTCTTACTCATCAATTCTTTC
133658 TTTTG
1 TTTTG
133663 GATTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 4 0.15
25 14 0.52
26 9 0.33
ACGTcount: A:0.13, C:0.18, G:0.05, T:0.64
Consensus pattern (26 bp):
TTTTGTTCTTACTCATCAATTCTTTC
Found at i:140075 original size:19 final size:19
Alignment explanation
Indices: 140051--140116 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
140041 TACATATATT
140051 ATTTTTTCCTTTCTTTTCA
1 ATTTTTTCCTTTCTTTTCA
140070 A--TTTT--TTTCTTATT--
1 ATTTTTTCCTTTCTT-TTCA
140084 ATTTTTTCCTTTCTTTTCA
1 ATTTTTTCCTTTCTTTTCA
*
140103 ATTTTTTTCTTTCT
1 ATTTTTTCCTTTCT
140117 CGATTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
14 1 0.03
15 6 0.15
16 6 0.15
17 6 0.15
18 6 0.15
19 14 0.36
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTTCCTTTCTTTTCA
Found at i:140088 original size:33 final size:33
Alignment explanation
Indices: 140047--140113 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
140037 TATATACATA
140047 TATTATTTTTTCCTTTCTTTTCAATTTTTTTCT
1 TATTATTTTTTCCTTTCTTTTCAATTTTTTTCT
140080 TATTATTTTTTCCTTTCTTTTCAATTTTTTTCT
1 TATTATTTTTTCCTTTCTTTTCAATTTTTTTCT
140113 T
1 T
140114 TCTCGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (33 bp):
TATTATTTTTTCCTTTCTTTTCAATTTTTTTCT
Found at i:140124 original size:16 final size:15
Alignment explanation
Indices: 140060--140126 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 15
140050 TATTTTTTCC
140060 TTTCTTTTCAATTTT
1 TTTCTTTTCAATTTT
*
140075 TTTCTTATT-ATTTTTT
1 TTTCTT-TTCA-ATTTT
140091 CCTTTCTTTTCAATTTT
1 --TTTCTTTTCAATTTT
*
140108 TTTCTTTCTCGATTTT
1 TTTCTTT-TCAATTTT
140124 TTT
1 TTT
140127 AATTGAGAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
15 14 0.33
16 16 0.37
17 6 0.14
18 7 0.16
ACGTcount: A:0.10, C:0.15, G:0.01, T:0.73
Consensus pattern (15 bp):
TTTCTTTTCAATTTT
Found at i:145555 original size:13 final size:13
Alignment explanation
Indices: 145525--145549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
145515 TTTTGAGCTG
145525 ACTTTTTTAACAC
1 ACTTTTTTAACAC
145538 ACTTTTTTAACA
1 ACTTTTTTAACA
145550 TCCTTTATCT
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:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
ACTTTTTTAACAC
Found at i:150823 original size:19 final size:19
Alignment explanation
Indices: 150799--150840 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
150789 ATCTACTATT
150799 CTTGCACCGACGGTGTACG
1 CTTGCACCGACGGTGTACG
150818 CTTGCACCGACGGTGTACG
1 CTTGCACCGACGGTGTACG
150837 CTTG
1 CTTG
150841 AACATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.31, G:0.31, T:0.24
Consensus pattern (19 bp):
CTTGCACCGACGGTGTACG
Found at i:156616 original size:19 final size:19
Alignment explanation
Indices: 156576--156618 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
156566 ACAACTGAAC
*
156576 AAACTACCGATACTTAAGA
1 AAACTACCGATACTTAACA
* *
156595 AAACTACTGATACTTTACA
1 AAACTACCGATACTTAACA
156614 AAACT
1 AAACT
156619 TCTACCAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (19 bp):
AAACTACCGATACTTAACA
Found at i:163691 original size:18 final size:18
Alignment explanation
Indices: 163670--163710 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
163660 TGTTATCAAA
163670 TTATTTTTTTATAA-ATGT
1 TTATTTTTTTA-AATATGT
163688 TTATTTTTTTAAATATGT
1 TTATTTTTTTAAATATGT
163706 TTATT
1 TTATT
163711 ATATTATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTTTTTTAAATATGT
Found at i:165516 original size:19 final size:17
Alignment explanation
Indices: 165476--165526 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
165466 GTTGATTTAG
165476 TTTGTTTTCATAAATTCTC
1 TTTGTTTT-A-AAATTCTC
165495 TTTGTTTTAAAACTTCTGC
1 TTTGTTTTAAAA-TTCT-C
165514 TTT-TCTTTAAAAT
1 TTTGT-TTTAAAAT
165527 AAGGTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 7 0.24
19 19 0.66
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTGTTTTAAAATTCTC
Found at i:166086 original size:30 final size:29
Alignment explanation
Indices: 166020--166085 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
166010 AATAGTTTAT
*
166020 ATTTTTATAATTTTTAAAGGATTAAATCA
1 ATTTTTATAATTTTTAAAGGATCAAATCA
* *
166049 ATTTTTTATAATTTTTAAGGGGTCAATATGCA
1 A-TTTTTATAATTTTTAAAGGATCAA-AT-CA
166081 ATTTT
1 ATTTT
166086 ACCTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 21 0.68
31 6 0.19
32 3 0.10
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (29 bp):
ATTTTTATAATTTTTAAAGGATCAAATCA
Found at i:166782 original size:18 final size:18
Alignment explanation
Indices: 166726--166796 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
166716 AATGGTTTCT
166726 TAAATAATTATTAAATTCTA
1 TAAATAATTATTAAA-T-TA
**
166746 TTAAATAATTACAAAAAATTA
1 -TAAATAATT--ATTAAATTA
166767 TATAA-AATTATTAAATTA
1 TA-AATAATTATTAAATTA
166785 TAAATAATTATT
1 TAAATAATTATT
166797 TATTTATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.05
18 16 0.38
20 6 0.14
21 13 0.31
22 1 0.02
23 4 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATAATTATTAAATTA
Found at i:166803 original size:18 final size:18
Alignment explanation
Indices: 166761--166812 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
166751 TAATTACAAA
166761 AAATTA-TATAAAATTATT
1 AAATTATTA-AAAATTATT
166779 AAATTA-TAAATAATTATT
1 AAATTATTAAA-AATTATT
* *
166797 TATTTATTAAAAATTA
1 AAATTATTAAAAATTA
166813 ATAATAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.80
19 4 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTAAAAATTATT
Found at i:166810 original size:28 final size:29
Alignment explanation
Indices: 166726--166812 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 29
166716 AATGGTTTCT
166726 TAAATAATTATTAAATTCTATTAAATAATTA
1 TAAATAATTATTAAATT-TATTAAA-AATTA
* * *
166757 CAAAAAATTATATAAAATTATT--AAATTA
1 TAAATAATTAT-TAAATTTATTAAAAATTA
*
166785 TAAATAATTATT-TATTTATTAAAAATTA
1 TAAATAATTATTAAATTTATTAAAAATTA
166813 ATAATAAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
26 6 0.13
27 1 0.02
28 20 0.43
29 1 0.02
31 13 0.28
32 5 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
TAAATAATTATTAAATTTATTAAAAATTA
Found at i:167134 original size:16 final size:16
Alignment explanation
Indices: 167113--167154 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
167103 AATATATATA
*
167113 TATATATTATTTTATT
1 TATATATTATATTATT
167129 TATATATTTATATTATT
1 TATATA-TTATATTATT
167146 T-TATATTAT
1 TATATATTAT
167155 CATATATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATATTATATTATT
Found at i:167135 original size:22 final size:23
Alignment explanation
Indices: 167107--167161 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
167097 TTTAATAATA
167107 TATATATATATATTATTTTAT-T
1 TATATATATATATTATTTTATAT
*
167129 TATATATTTATATTATTTTATAT
1 TATATATATATATTATTTTATAT
167152 TATCATATAT
1 TAT-ATATAT
167162 GTTATCTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 4 0.14
24 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATATATATATTATTTTATAT
Found at i:167159 original size:18 final size:17
Alignment explanation
Indices: 167111--167152 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
167101 ATAATATATA
*
167111 TATATATATTATTTTATT
1 TATATAT-TTATATTATT
167129 TATATATTTATATTATT
1 TATATATTTATATTATT
167146 T-TATATT
1 TATATATT
167153 ATCATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.26
17 10 0.43
18 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATATTTATATTATT
Found at i:167166 original size:22 final size:21
Alignment explanation
Indices: 167104--167166 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
167094 TTTTTTAATA
167104 ATATATATATATATATTATTTT
1 ATAT-TATATATATATTATTTT
167126 AT-TTATATATTTATATTATTTT
1 ATATTATATA--TATATTATTTT
*
167148 ATATTATCATATATGTTAT
1 ATATTAT-ATATATATTAT
167167 CTATAATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 22 0.61
23 4 0.11
24 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATTATATATATATTATTTT
Found at i:167490 original size:2 final size:2
Alignment explanation
Indices: 167483--167515 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
167473 GGTTAAATAC
167483 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
167516 ATTAAAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:174769 original size:149 final size:148
Alignment explanation
Indices: 174481--175277 Score: 889
Period size: 149 Copynumber: 5.4 Consensus size: 148
174471 TTATTAAAAC
** * ** * *
174481 AAAATCACTGTTTTACTTCAAAAT-CAAA-ACTTATTTCGAAATAGTT--AAAGATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
* * *
174542 GTTTAAAAATTTAAA-TTTTCTCTTTAAAATCACTAAAAAAATTAATTTT-TTTTT--AAATCT-
66 GTTTAAAAATTTAAACTTTT-TCTTTAAAATGACTAAAAACA-TATTTTTATTTTTAAAAATCTA
174602 AA----A--TTTTTTTAATG
129 AACTTTATTTTTTTTTAATG
* *
174616 AAAATTACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAAATCTAAATTT
1 AAAATCACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTT-AAAAAAATCAAAATTT
* *
174681 TGTTTAAAAATTCAAAC-TTTTCTTTAAAATGACTAAAAACATATTTTTATTTTTTTAAAATCTA
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAACATATTTTTA-TTTTTAAAAATCTA
174745 AACTTTATTTTTTTTTAATG
129 AACTTTATTTTTTTTTAATG
* * * ** * *
174765 AAAATAACTATTTTACTTAAAAATCCAAACTTTCGTTTTGAAATAGTTAAAAAAAACCAAAATTT
1 AAAATCACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTT-AAAAAAATCAAAATTT
* * *
174830 TGTTTAAAATTTTAAAATTTTTCTTTAAAATGACTAAAAAACAGATTTTTTATTTTTTAAAAATC
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATGACT-AAAAACATA-TTTTTA-TTTTTAAAAATC
* *
174895 TAAATTTTCTTTTTTTTTAATG
127 TAAACTTTATTTTTTTTTAATG
*
174917 AAAATCACTACTTTACTTAGAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
1 AAAATCACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
* * * *
174982 GTTTAAAATTTTAAACTTTTTTTTTTAAATGACAAAAAACATA-TTTTATTTTT-AAAATCTAAA
66 GTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAA
* *
175045 CTTTA-TCTTTTTTAAAG
131 CTTTATTTTTTTTTAATG
* * * * * * *
175062 AAATTCAGTATTTTACTTAAAAATCTAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
* * *
175127 GTTTAAACATTTAAACTTTTTTCTTTAAAATGACTAAAAACAAATTTTTATTTTTAAAAATATAA
66 GTTTAAAAATTTAAAC-TTTTTCTTTAAAATGACTAAAAACATATTTTTATTTTTAAAAATCTAA
* * *
175192 ACTTT-CTCTTTTTTAAAG
130 ACTTTATTTTTTTTTAATG
* * *
175210 AAAATCACTA-TTATTCTTAAAAAATCAAAATTTTTATTTCGAAATTGTTTAAAAAAATCAAAAC
1 AAAATCACTACTT-TACTT-AAAAATCCAAATTTTTATTTCGAAATAG-TTAAAAAAATCAAAA-
175274 TTTT
62 TTTT
175278 TCCCTAGATC
Statistics
Matches: 566, Mismatches: 68, Indels: 40
0.84 0.10 0.06
Matches are distributed among these distances:
135 20 0.04
136 4 0.01
137 16 0.03
138 6 0.01
139 19 0.03
140 34 0.06
142 6 0.01
143 2 0.00
145 81 0.14
146 36 0.06
147 18 0.03
148 42 0.07
149 106 0.19
150 40 0.07
151 57 0.10
152 79 0.14
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (148 bp):
AAAATCACTACTTTACTTAAAAATCCAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTT
GTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAACATATTTTTATTTTTAAAAATCTAAA
CTTTATTTTTTTTTAATG
Found at i:175693 original size:3 final size:3
Alignment explanation
Indices: 175685--175713 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
175675 ATGAAACATT
175685 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
175714 TTGAGCCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:175749 original size:11 final size:11
Alignment explanation
Indices: 175733--175759 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
175723 TGACAAACCC
175733 AAAAAGAAAAG
1 AAAAAGAAAAG
175744 AAAAAGAAAAG
1 AAAAAGAAAAG
175755 AAAAA
1 AAAAA
175760 CAAATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:179608 original size:19 final size:19
Alignment explanation
Indices: 179586--179635 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
179576 TTATATTAGG
179586 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATAT
* *
179605 ATTTATTATTTAAATTTAT
1 ATTTAATATTTAAATATAT
179624 ATTTAA-ATTTAA
1 ATTTAATATTTAA
179636 TTTATGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTAATATTTAAATATAT
Found at i:179626 original size:12 final size:12
Alignment explanation
Indices: 179605--179639 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
179595 TTAAGATATT
179605 ATTTATTATTTAA
1 ATTTA-TATTTAA
179618 ATTTATATTTAA
1 ATTTATATTTAA
179630 ATTTA-ATTTA
1 ATTTATATTTA
179640 TGTTTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 5 0.23
12 12 0.55
13 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTATATTTAA
Found at i:179637 original size:17 final size:18
Alignment explanation
Indices: 179612--179645 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
179602 ATTATTTATT
179612 ATTTAAATTTATATTTAA
1 ATTTAAATTTATATTTAA
*
179630 ATTT-AATTTATGTTTA
1 ATTTAAATTTATATTTA
179646 TCTTTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTAAATTTATATTTAA
Found at i:186093 original size:18 final size:18
Alignment explanation
Indices: 186054--186102 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
186044 GACACCCAAT
***
186054 TATTTTTATTTTTATTTT
1 TATTTTTATTTTTATAAC
186072 TATTTTTATTTTTATAAC
1 TATTTTTATTTTTATAAC
186090 TA--TTTATTTTTAT
1 TATTTTTATTTTTAT
186103 TTGTCCAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 11 0.39
18 17 0.61
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTATTTTTATAAC
Found at i:186104 original size:6 final size:6
Alignment explanation
Indices: 186053--186086 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
186043 AGACACCCAA
186053 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTAT
186087 AACTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Done.