Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003589.1 Kokia drynarioides strain JFW-HI SEQ_116463, 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: 21181
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:364 original size:3 final size:3
Alignment explanation
Indices: 350--416 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
340 CCTTTTAGTT
* * * * *
350 TTA TTT TTA TTA TTA ATA TTA ATA TTAA TTA ATA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
396 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
417 ATGTCATTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1175 original size:16 final size:16
Alignment explanation
Indices: 1154--1206 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
1144 GTTTTTGGAC
* *
1154 TTTTAATTTAATTAAG
1 TTTTAATTAAATTAAA
* *
1170 TTTTAAATCAATTTAAA
1 TTTT-AATTAAATTAAA
1187 TTTTAATTAAATTTAAA
1 TTTTAATTAAA-TTAAA
1204 TTT
1 TTT
1207 AAAGCAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAATTAAATTAAA
Found at i:1190 original size:17 final size:17
Alignment explanation
Indices: 1165--1242 Score: 77
Period size: 17 Copynumber: 4.5 Consensus size: 17
1155 TTTAATTTAA
* *
1165 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
1182 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
1199 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
1216 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
1235 TTAAATTT
1 TTAAATTT
1243 AAAAATACAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 5 0.10
17 28 0.56
18 2 0.04
19 14 0.28
20 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:1194 original size:6 final size:6
Alignment explanation
Indices: 1179--1245 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
1169 GTTTTAAATC
* **
1179 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
**
1226 AAGATA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
1246 AATACATTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 7 0.15
6 37 0.77
7 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:1236 original size:19 final size:18
Alignment explanation
Indices: 1179--1246 Score: 86
Period size: 17 Copynumber: 3.8 Consensus size: 18
1169 GTTTTAAATC
* *
1179 AATTTAAATTT-TAATTA
1 AATTTAAATTTAAAAGTA
*
1196 AATTTAAATTT-AAAGCA
1 AATTTAAATTTAAAAGTA
1213 AATTTAAATTTAAAAGATA
1 AATTTAAATTTAAAAG-TA
1232 AATTTAAATTTAAAA
1 AATTTAAATTTAAAA
1247 ATACATTTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 25 0.56
18 4 0.09
19 16 0.36
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (18 bp):
AATTTAAATTTAAAAGTA
Found at i:2059 original size:169 final size:168
Alignment explanation
Indices: 1722--2083 Score: 465
Period size: 169 Copynumber: 2.1 Consensus size: 168
1712 GGATTTGGTT
* * * * * *
1722 CACTTCTCAGTATTTCAACAGGAAACTAACCATTTATTGCTTCGACCTGCTTCTCAGTATCTCAT
1 CACTTCTCTGTATCTCATCAGGAAGCTAACCATTTAATGCTTCGACCTACTTCTCAGTATCTCAT
* * *
1787 CAGGAGGCTGGGGTTCGAAGATTTGCTCACGTCGAGCGTGGGTTTGTTTTGGTCTTCTTCTCAAT
66 CAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAAT
* *
1852 ATTTCATCAGGAAGATGACCGTATCGCTTACATCAATC
131 ATCTCATCAGGAAGATGACCGCATCGCTTACATCAATC
* *
1890 CACTTCTTTGTATCTCATCAGGAAGCTAATCATTTTAATGCTTCG-CCTTACTTCTCAGTATCTC
1 CACTTCTCTGTATCTCATCAGGAAGCTAACCA-TTTAATGCTTCGACC-TACTTCTCAGTATCTC
* * * * *
1954 ATCAGGAAGTTGGGGTTCGAATATTTGTTCGCATTGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
64 ATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCA
* * * * ***
2019 GTATCTCATCGGGAAGGTGACCGCATTGCTTGTTTCAATC
129 ATATCTCATCAGGAAGATGACCGCATCGCTTACATCAATC
*
2059 CGCTTCTCTGTATCTCATCAGGAAG
1 CACTTCTCTGTATCTCATCAGGAAG
2084 ACGAATTTGG
Statistics
Matches: 165, Mismatches: 27, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
168 28 0.17
169 137 0.83
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (168 bp):
CACTTCTCTGTATCTCATCAGGAAGCTAACCATTTAATGCTTCGACCTACTTCTCAGTATCTCAT
CAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAAT
ATCTCATCAGGAAGATGACCGCATCGCTTACATCAATC
Found at i:9832 original size:21 final size:21
Alignment explanation
Indices: 9806--9882 Score: 86
Period size: 21 Copynumber: 3.6 Consensus size: 21
9796 TAACTGGCTA
9806 TATTTTTCCTCTAATCGCCTG
1 TATTTTTCCTCTAATCGCCTG
* * *
9827 TATTTTACCT-TGCATCGCGTCG
1 TATTTTTCCTCT-AATCGCCT-G
9849 -ATTTTCTCCTCTAATCGCCTG
1 TATTTT-TCCTCTAATCGCCTG
9870 TATTTTTCCTCTA
1 TATTTTTCCTCTA
9883 TTTATCTAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 28 0.62
22 15 0.33
23 1 0.02
ACGTcount: A:0.14, C:0.29, G:0.10, T:0.47
Consensus pattern (21 bp):
TATTTTTCCTCTAATCGCCTG
Found at i:13738 original size:58 final size:59
Alignment explanation
Indices: 13676--13813 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 59
13666 ATTTTGCCTT
* * * *
13676 TTCGAGGGCAAAATGGTAATTTCGAGAAAG-TTCGGGGT-TAAAATTGGA-ATTTTAGACA
1 TTCGAGGGCAAAATGGTAATTTCGAG--AGTTTCGAGGTCAAAAAATAGAGATTTTAGACA
** * * *
13734 TTCGAGGATAAAAGGGTAATTTTGAGAGTTTCGAGGTCAAAAAATAGAGTTTTTAGACA
1 TTCGAGGGCAAAATGGTAATTTCGAGAGTTTCGAGGTCAAAAAATAGAGATTTTAGACA
13793 TTCGAGGGC-AAATGGTAATTT
1 TTCGAGGGCAAAATGGTAATTT
13814 TTGAAAGTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
56 2 0.03
57 7 0.11
58 40 0.62
59 16 0.25
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (59 bp):
TTCGAGGGCAAAATGGTAATTTCGAGAGTTTCGAGGTCAAAAAATAGAGATTTTAGACA
Found at i:13892 original size:29 final size:29
Alignment explanation
Indices: 13855--14087 Score: 168
Period size: 30 Copynumber: 7.9 Consensus size: 29
13845 GGATGCTCGA
13855 GGGT-AAAAATAT-AATTTTTGGAAGTTTT
1 GGGTCAAAAAT-TGAATTTTTGGAAGTTTT
* * * *
13883 GGGCTCAAAAATGGAATTTTAGAAATTTTT
1 GGG-TCAAAAATTGAATTTTTGGAAGTTTT
*
13913 GTGTCAAAAATTGAATTTTTGGAAGTTTT
1 GGGTCAAAAATTGAATTTTTGGAAGTTTT
*
13942 GGGGTCAAAAATTGAATTTTTGGAAGTTTC
1 -GGGTCAAAAATTGAATTTTTGGAAGTTTT
* * * *
13972 GAAGT-TAAAATGGAATTTTTGAAAGTTTT
1 G-GGTCAAAAATTGAATTTTTGGAAGTTTT
** * * *
14001 GGGGTTTAAAATGGAATTTTTAGAAGTTTC
1 -GGGTCAAAAATTGAATTTTTGGAAGTTTT
* * * * **
14031 GAGGTTAAAAATGGAATTTTTAGAAATTCGA
1 G-GGTCAAAAATTGAATTTTTGGAAGTT-TT
* *
14062 GGGT-AAACATGGAATTTTTGGAAGTT
1 GGGTCAAAAATTGAATTTTTGGAAGTT
14088 CGGGGGTAAA
Statistics
Matches: 169, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
28 3 0.02
29 66 0.39
30 99 0.59
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (29 bp):
GGGTCAAAAATTGAATTTTTGGAAGTTTT
Found at i:13901 original size:30 final size:29
Alignment explanation
Indices: 13802--14117 Score: 233
Period size: 29 Copynumber: 10.7 Consensus size: 29
13792 ATTCGAGGGC
* * **
13802 AAATGGTAATTTTTGAAAGTTTTAGGGCCA
1 AAATGG-AATTTTTGGAAGTTTTGGGGTAA
* * * *
13832 AAATGGAAATTTTGGATG-CTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTTG-GGGTAA
** *
13861 AAATATAATTTTTGGAAGTTTTGGGCTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGT-AA
* * * *
13891 AAATGGAA-TTTTAGAAATTTTTGTGTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGT-AA
*
13920 AAATTGAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGT-AA
* * ** *
13950 AAATTGAATTTTTGGAAGTTTCGAAGTTA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
* *
13979 AAATGGAATTTTTGAAAGTTTTGGGGTTTA
1 AAATGGAATTTTTGGAAGTTTTGGGG-TAA
* * *
14009 AAATGGAATTTTTAGAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGGAAGTTTTG-GGGTAA
* * *
14039 AAATGGAATTTTTAGAA-ATTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTTG-GGGTAA
* **
14068 ACATGGAATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
* *
14097 ACATGGAATTTTTGGGAGTTT
1 AAATGGAATTTTTGGAAGTTT
14118 AGGGACCTTC
Statistics
Matches: 229, Mismatches: 50, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
28 1 0.00
29 125 0.55
30 101 0.44
31 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTTGGGGTAA
Found at i:13930 original size:59 final size:59
Alignment explanation
Indices: 13857--14051 Score: 207
Period size: 59 Copynumber: 3.3 Consensus size: 59
13847 ATGCTCGAGG
* * * *
13857 GTAAAAATAT-AATTTTTGGAAGTTTTGGGCTCAAAAATGGAATTTTAGAAATTTTTG-T
1 GTAAAAAT-TGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTAGAAAGTTTCGAA
* * *
13915 GTCAAAAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATTGAATTTTTGGAAGTTTCGAA
1 GT-AAAAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTAGAAAGTTTCGAA
* * * ** *
13975 GTTAAAATGGAATTTTTGAAAGTTTTGGGGTTTAAAATGGAATTTTTAG-AAGTTTCGAG
1 GTAAAAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAA-TTTTAGAAAGTTTCGAA
*
14034 GTTAAAAATGGAATTTTT
1 G-TAAAAATTGAATTTTT
14052 AGAAATTCGA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 3 0.03
59 91 0.78
60 22 0.19
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (59 bp):
GTAAAAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTAGAAAGTTTCGAA
Found at i:14074 original size:59 final size:58
Alignment explanation
Indices: 13802--14110 Score: 198
Period size: 59 Copynumber: 5.2 Consensus size: 58
13792 ATTCGAGGGC
** ** * * * *
13802 AAATGGTAATTTTTGAAAGTTTTAGGGCCAAAATGGAAATTTTGGATG-CTCGAGGGTAA
1 AAATGG-AATTTTTGAAAG-TTCGGGGTTAAAATGGAATTTTTGGAAGTTTCGAGGTTAA
** * * * * * * * * * *
13861 AAATATAATTTTTGGAAGTTTTGGGCTCAAAAATGGAATTTTAGAAATTTTTG-TGTCAA
1 AAATGGAATTTTTGAAAG-TTCGGGGT-TAAAATGGAATTTTTGGAAGTTTCGAGGTTAA
* * * * * *
13920 AAATTGAATTTTTGGAAGTTTTGGGGTCAAAAATTGAATTTTTGGAAGTTTCGAAGTT-A
1 AAATGGAATTTTTGAAAG-TTCGGGGT-TAAAATGGAATTTTTGGAAGTTTCGAGGTTAA
* *
13979 AAATGGAATTTTTGAAAGTTTTGGGGTTTAAAATGGAATTTTTAGAAGTTTCGAGGTTAA
1 AAATGGAATTTTTGAAAG-TTCGGGG-TTAAAATGGAATTTTTGGAAGTTTCGAGGTTAA
* *
14039 AAATGGAATTTTTAGAAA-TTCGAGGG-TAAACATGGAATTTTTGGAAG-TTCGGGGGTAA
1 AAATGGAATTTTT-GAAAGTTCG-GGGTTAAA-ATGGAATTTTTGGAAGTTTCGAGGTTAA
*
14097 ACATGGAATTTTTG
1 AAATGGAATTTTTG
14111 GGAGTTTAGG
Statistics
Matches: 204, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
57 1 0.00
58 42 0.21
59 135 0.66
60 22 0.11
61 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (58 bp):
AAATGGAATTTTTGAAAGTTCGGGGTTAAAATGGAATTTTTGGAAGTTTCGAGGTTAA
Found at i:15126 original size:3 final size:3
Alignment explanation
Indices: 15112--15181 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
15102 CCTTTCGGTT
* * * * *
15112 TTA TTT TTA TTA TTA ATA TTA ATA TTAA TTA ATA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* *
15158 -CA ATA TTTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA
15182 ATGTCATTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
2 1 0.02
3 45 0.88
4 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:15144 original size:16 final size:15
Alignment explanation
Indices: 15119--15183 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 15
15109 GTTTTATTTT
15119 TATTATTAATATTAA
1 TATTATTAATATTAA
15134 TATTAATTAATATT-A
1 TATT-ATTAATATTAA
*
15149 TCATTATTACAATATTTAT
1 T-ATTATT--AATA-TTAA
*
15168 TATTATTATTATTAA
1 TATTATTAATATTAA
15183 T
1 T
15184 GTCATTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
15 13 0.32
16 15 0.37
17 4 0.10
18 8 0.20
19 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTATTAATATTAA
Found at i:15192 original size:16 final size:16
Alignment explanation
Indices: 15172--15212 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
15162 ATTTATTATT
15172 ATTATTATTAAT-GTC
1 ATTATTATTAATGGTC
*
15187 ATTTATTGTT-ATGGTC
1 A-TTATTATTAATGGTC
15203 ATTATTATTA
1 ATTATTATTA
15213 TTAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (16 bp):
ATTATTATTAATGGTC
Found at i:15407 original size:17 final size:16
Alignment explanation
Indices: 15387--15419 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
15377 GTATTGAAGC
15387 AATGCCTGAATGATTTT
1 AATGCCTGAAT-ATTTT
15404 AATGCCTGAATATTTT
1 AATGCCTGAATATTTT
15420 GGGTCTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (16 bp):
AATGCCTGAATATTTT
Found at i:15987 original size:18 final size:17
Alignment explanation
Indices: 15922--15989 Score: 75
Period size: 17 Copynumber: 3.8 Consensus size: 17
15912 ATTAAGTTTT
15922 AAATCAATTTAAATTTAA
1 AAAT-AATTTAAATTTAA
*
15940 AGCA-AATTTAAATTTAA
1 A-AATAATTTAAATTTAA
15957 AAGATAAATTTAAATTTAA
1 AA-AT-AATTTAAATTTAA
15976 AAATACATTTAAAT
1 AAATA-ATTTAAAT
15990 CAATTTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
17 16 0.37
18 11 0.26
19 16 0.37
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (17 bp):
AAATAATTTAAATTTAA
Found at i:17516 original size:20 final size:22
Alignment explanation
Indices: 17493--17537 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
17483 ATATTTTTTA
*
17493 TTTCTA-TAAA-ATTTTGAAAT
1 TTTCTAGTAAATATTTTAAAAT
17513 TTTCTAGTAAATATTTTAAAAT
1 TTTCTAGTAAATATTTTAAAAT
17535 TTT
1 TTT
17538 GAAGATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTCTAGTAAATATTTTAAAAT
Found at i:20403 original size:19 final size:20
Alignment explanation
Indices: 20376--20417 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
20366 ATATATTTTA
20376 TTTTTAT-A-ATTTAATTAT
1 TTTTTATAATATTTAATTAT
20394 TTTTTAATAATATTTAATTAT
1 TTTTT-ATAATATTTAATTAT
20415 TTT
1 TTT
20418 ATATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 2 0.10
20 1 0.05
21 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATAATATTTAATTAT
Done.