Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014487.1 Kokia drynarioides strain JFW-HI SEQ_129526, 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: 39003
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Found at i:1555 original size:10 final size:10
Alignment explanation
Indices: 1540--1574 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
1530 ATTTAAAAAA
1540 AAAAAAATCG
1 AAAAAAATCG
1550 -AAAAAAT-G
1 AAAAAAATCG
1558 AAAAAAATCG
1 AAAAAAATCG
1568 AAAAAAA
1 AAAAAAA
1575 AATTTAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.04
9 14 0.61
10 8 0.35
ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09
Consensus pattern (10 bp):
AAAAAAATCG
Found at i:2656 original size:23 final size:25
Alignment explanation
Indices: 2630--2676 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2620 TCCAATTAGG
2630 AAATTAT-TGTTTAG-ATTTAATTC
1 AAATTATCTGTTTAGAATTTAATTC
*
2653 AAATTATCTTTTTAGAATTTAATT
1 AAATTATCTGTTTAGAATTTAATT
2677 TGGATCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (25 bp):
AAATTATCTGTTTAGAATTTAATTC
Found at i:9153 original size:70 final size:71
Alignment explanation
Indices: 9039--9188 Score: 266
Period size: 70 Copynumber: 2.1 Consensus size: 71
9029 ACAAGAACTA
9039 AAAATAAAGTAAAATTAAAAAAAAAAAAATAGAGTGAACAATAAAACTTCCGTAAAAGCTTCAAA
1 AAAATAAAGTAAAATTAAAAAAAAAAAAATAGAGTGAACAATAAAACTTCCGTAAAAGCTTCAAA
9104 AACCTC
66 AACCTC
** *
9110 AAAATAAAGTAAAATT-GGAAAAAAAAAATAGAGTGAACAATAAAGCTTCCGTAAAAGCTTCAAA
1 AAAATAAAGTAAAATTAAAAAAAAAAAAATAGAGTGAACAATAAAACTTCCGTAAAAGCTTCAAA
9174 AACCTC
66 AACCTC
9180 AAAATAAAG
1 AAAATAAAG
9189 ATTTTTTTAA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 60 0.79
71 16 0.21
ACGTcount: A:0.59, C:0.12, G:0.11, T:0.18
Consensus pattern (71 bp):
AAAATAAAGTAAAATTAAAAAAAAAAAAATAGAGTGAACAATAAAACTTCCGTAAAAGCTTCAAA
AACCTC
Found at i:11358 original size:25 final size:25
Alignment explanation
Indices: 11330--11379 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
11320 CCTTTTTAAA
*
11330 ATATATATAT-ATTTTCTTTTTTATT
1 ATATATATATAATATT-TTTTTTATT
11355 ATATATATATAATATTTTTTTTATT
1 ATATATATATAATATTTTTTTTATT
11380 TTGCTTAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
ATATATATATAATATTTTTTTTATT
Found at i:11372 original size:23 final size:22
Alignment explanation
Indices: 11331--11378 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
11321 CTTTTTAAAA
** *
11331 TATATATATATTTTCTTTTTTAT
1 TATATATATATAATATTTTTT-T
11354 TATATATATATAATATTTTTTT
1 TATATATATATAATATTTTTTT
11376 TAT
1 TAT
11379 TTTGCTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATATATATATAATATTTTTTT
Found at i:17149 original size:15 final size:14
Alignment explanation
Indices: 17093--17149 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
17083 TCACTTTTTT
17093 TTATTAAAAAAATA
1 TTATTAAAAAAATA
*
17107 TTATGTAAAATAATAA
1 TTAT-TAAAAAAAT-A
*
17123 TTA-CAAAAAAATA
1 TTATTAAAAAAATA
*
17136 TTATGTAAACAAAT
1 TTAT-TAAAAAAAT
17150 CCCAACTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.12
14 11 0.32
15 15 0.44
16 4 0.12
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (14 bp):
TTATTAAAAAAATA
Found at i:21079 original size:2 final size:2
Alignment explanation
Indices: 21072--21098 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21062 AATTTTGGAT
21072 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 T
21099 TTTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21750 original size:29 final size:30
Alignment explanation
Indices: 21714--21782 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
21704 AATTAAAAAA
* *
21714 AATCAATTGAATTCTTAATTGAAAA-TT-AC
1 AATCAATTGAACTCTTAA-TCAAAAGTTGAC
*
21743 AATCAATTTAACTCTTAATCAAAAGTTGAC
1 AATCAATTGAACTCTTAATCAAAAGTTGAC
21773 AATCAATTGA
1 AATCAATTGA
21783 GTCCTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.15
29 18 0.53
30 11 0.32
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (30 bp):
AATCAATTGAACTCTTAATCAAAAGTTGAC
Found at i:22221 original size:151 final size:151
Alignment explanation
Indices: 22057--22357 Score: 541
Period size: 151 Copynumber: 2.0 Consensus size: 151
22047 GAAAGAATAG
22057 TAAAAAAGTTATAAAAAAACATTACATAATTTTAAAATATATATGTTATTTTGAATTTTAGAGTT
1 TAAAAAAGTTATAAAAAAACATTACATAATTTTAAAATATATATGTTATTTTGAATTTTAGAGTT
* * *
22122 TATTGTTTTTATAATAAAGAAATTGGGGAATTTAAAGTATAATGGTGATTAGATTTGTATGAG-G
66 TATTATTTTTATAATAAAGAAATTGGGAAATTTAAAGTATAATGGTGATTAGACTTGTATGAGAG
*
22186 TGTCGAGTGAAAATGAGTTTAT
131 -GTCGAGTGAAAATGAATTTAT
22208 TAAAAAAGTTATAAAAAAACATTACATAATTTTAAAATATATATGTTATTTTGAATTTTAGAGTT
1 TAAAAAAGTTATAAAAAAACATTACATAATTTTAAAATATATATGTTATTTTGAATTTTAGAGTT
*
22273 TATTATTTTTATAATAAAGAAATTGGGAAATTTAAAGTATGATGGTGATTAGACTTGTATGAGAG
66 TATTATTTTTATAATAAAGAAATTGGGAAATTTAAAGTATAATGGTGATTAGACTTGTATGAGAG
22338 GTCGAGTGAAAATGAATTTA
131 GTCGAGTGAAAATGAATTTA
22358 ATATTTGACG
Statistics
Matches: 144, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
151 143 0.99
152 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (151 bp):
TAAAAAAGTTATAAAAAAACATTACATAATTTTAAAATATATATGTTATTTTGAATTTTAGAGTT
TATTATTTTTATAATAAAGAAATTGGGAAATTTAAAGTATAATGGTGATTAGACTTGTATGAGAG
GTCGAGTGAAAATGAATTTAT
Found at i:22526 original size:10 final size:10
Alignment explanation
Indices: 22513--22577 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
22503 AAAATGCTAC
*
22513 AAAAATTTTA
1 AAAAATTATA
22523 AAAAATTATA
1 AAAAATTATA
*
22533 AAAATAATATTA
1 AAAA-ATTA-TA
* *
22545 TAAAATTATT
1 AAAAATTATA
*
22555 AAATATTATA
1 AAAAATTATA
22565 ACAAAATT-TA
1 A-AAAATTATA
22575 AAA
1 AAA
22578 GTACAACTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.58
11 11 0.26
12 5 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTATA
Found at i:22663 original size:22 final size:20
Alignment explanation
Indices: 22638--22709 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 20
22628 TTAATAAATT
22638 TAATAATTTTTTATCATTTTGA
1 TAATAATTTTTTAT-ATTTT-A
*
22660 TAAT-TTTTATTTA-ATTTTA
1 TAATAATTT-TTTATATTTTA
22679 T-ATAATTTTTTATAGTTTTTA
1 TAATAATTTTTTATA--TTTTA
*
22700 AAATAATTTT
1 TAATAATTTT
22710 CTAAAACATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 6 0.15
19 6 0.15
20 5 0.12
21 8 0.20
22 16 0.39
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (20 bp):
TAATAATTTTTTATATTTTA
Found at i:22667 original size:10 final size:9
Alignment explanation
Indices: 22615--22699 Score: 53
Period size: 9 Copynumber: 8.7 Consensus size: 9
22605 TTTAAATTTT
*
22615 TTTTTGTAA
1 TTTTTATAA
22624 TTTTTTAATAA
1 -TTTTT-ATAA
* *
22635 ATTTAATAA
1 TTTTTATAA
*
22644 TTTTTTATCA
1 -TTTTTATAA
*
22654 TTTTGATAA
1 TTTTTATAA
22663 TTTTTATTTAA
1 TTTTTA--TAA
22674 TTTTATATAA
1 TTTT-TATAA
*
22684 TTTTTTATAG
1 -TTTTTATAA
22694 TTTTTA
1 TTTTTA
22700 AAATAATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
9 22 0.37
10 21 0.36
11 14 0.24
12 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:22676 original size:11 final size:11
Alignment explanation
Indices: 22659--22709 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
22649 TATCATTTTG
22659 ATAATTTTTAT
1 ATAATTTTTAT
*
22670 TTAA-TTTTAT
1 ATAATTTTTAT
22680 ATAATTTTT-T
1 ATAATTTTTAT
* *
22690 ATAGTTTTTAAA
1 ATAATTTTT-AT
22702 ATAATTTT
1 ATAATTTT
22710 CTAAAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 18 0.56
11 7 0.22
12 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATAATTTTTAT
Found at i:22697 original size:20 final size:19
Alignment explanation
Indices: 22621--22697 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 19
22611 TTTTTTTTTG
*
22621 TAATTTTTTAATAAATTTAA
1 TAATTTTTT-ATAATTTTAA
* *
22641 TAATTTTTTATCATTTTGA
1 TAATTTTTTATAATTTTAA
*
22660 TAATTTTTATTTAATTTTATA
1 TAATTTTT-TATAATTTTA-A
*
22681 TAATTTTTTATAGTTTT
1 TAATTTTTTATAATTTT
22698 TAAAATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 15 0.32
20 23 0.49
21 9 0.19
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (19 bp):
TAATTTTTTATAATTTTAA
Found at i:23217 original size:6 final size:6
Alignment explanation
Indices: 23208--23235 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
23198 TGATATATCG
23208 ATTTGT ATTTGT ATTTGT ATTTGT ATTT
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTT
23236 TTTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
ATTTGT
Found at i:24743 original size:24 final size:24
Alignment explanation
Indices: 24722--24789 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
24712 ATCTTTCAGC
*
24722 TAAACTCTGTTTAATTGTTTCAAT
1 TAAACTCTGTTTATTTGTTTCAAT
*
24746 TAAACTCTGTTTATTTGCTTCAAT
1 TAAACTCTGTTTATTTGTTTCAAT
*
24770 TAAATTCTGTTTATTTGTTT
1 TAAACTCTGTTTATTTGTTT
24790 GAGTCAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (24 bp):
TAAACTCTGTTTATTTGTTTCAAT
Found at i:26720 original size:24 final size:24
Alignment explanation
Indices: 26693--26743 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
26683 AGAAATAATC
*
26693 TTTCAGCTAAACTCTATTTAATTG
1 TTTCAACTAAACTCTATTTAATTG
* * *
26717 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAACTAAACTCTATTTAATTG
26741 TTT
1 TTT
26744 AAGTCAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.53
Consensus pattern (24 bp):
TTTCAACTAAACTCTATTTAATTG
Found at i:26752 original size:24 final size:24
Alignment explanation
Indices: 26701--26755 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
26691 TCTTTCAGCT
*
26701 AAACTCTATTTAATTGTTTCAATT
1 AAACTCTATTTAATTGTTTCAATC
* *
26725 AAACTCTGTTTATTTGTTT-AAGTC
1 AAACTCTATTTAATTGTTTCAA-TC
26749 AAACTCT
1 AAACTCT
26756 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (24 bp):
AAACTCTATTTAATTGTTTCAATC
Found at i:28214 original size:31 final size:31
Alignment explanation
Indices: 28179--28237 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
28169 TACAATAGGG
* * *
28179 TTAATATGCCATTTGGTACTTGGGTTTGGTT
1 TTAATATGCAATTCGGTACTTGAGTTTGGTT
* *
28210 TTAATGTTCAATTCGGTACTTGAGTTTG
1 TTAATATGCAATTCGGTACTTGAGTTTG
28238 ACTTCAATGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (31 bp):
TTAATATGCAATTCGGTACTTGAGTTTGGTT
Found at i:28259 original size:31 final size:31
Alignment explanation
Indices: 28189--28259 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
28179 TTAATATGCC
* ** *
28189 ATTTGGTACTTGGGTTTGGTTTTAATGTTCA
1 ATTTGGTACTTGAGTTTGACTTCAATGTTCA
* *
28220 ATTCGGTACTTGAGTTTGACTTCAATGTTTA
1 ATTTGGTACTTGAGTTTGACTTCAATGTTCA
*
28251 TTTTGGTAC
1 ATTTGGTAC
28260 CTGTTATACA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.10, G:0.23, T:0.49
Consensus pattern (31 bp):
ATTTGGTACTTGAGTTTGACTTCAATGTTCA
Found at i:28640 original size:112 final size:112
Alignment explanation
Indices: 28443--28674 Score: 464
Period size: 112 Copynumber: 2.1 Consensus size: 112
28433 ATACCAAATT
28443 AAATATTAAAGCTAAACTCAGAAACTGATGTCATCACTCATCACTATATGTTTTTATATTGTTGC
1 AAATATTAAAGCTAAACTCAGAAACTGATGTCATCACTCATCACTATATGTTTTTATATTGTTGC
28508 ATTATTTGGTGGAATTTTCATGTAATGTCATTCTCTTATACTTTTAC
66 ATTATTTGGTGGAATTTTCATGTAATGTCATTCTCTTATACTTTTAC
28555 AAATATTAAAGCTAAACTCAGAAACTGATGTCATCACTCATCACTATATGTTTTTATATTGTTGC
1 AAATATTAAAGCTAAACTCAGAAACTGATGTCATCACTCATCACTATATGTTTTTATATTGTTGC
28620 ATTATTTGGTGGAATTTTCATGTAATGTCATTCTCTTATACTTTTAC
66 ATTATTTGGTGGAATTTTCATGTAATGTCATTCTCTTATACTTTTAC
28667 AAATATTA
1 AAATATTA
28675 TACCAAAGTA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 120 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (112 bp):
AAATATTAAAGCTAAACTCAGAAACTGATGTCATCACTCATCACTATATGTTTTTATATTGTTGC
ATTATTTGGTGGAATTTTCATGTAATGTCATTCTCTTATACTTTTAC
Found at i:29514 original size:2 final size:2
Alignment explanation
Indices: 29507--29532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29497 CAAGTTTACC
29507 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29533 GACCAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34827 original size:16 final size:16
Alignment explanation
Indices: 34806--34838 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34796 CATTCTGTTG
34806 GCTTAAGACAAATCAA
1 GCTTAAGACAAATCAA
34822 GCTTAAGACAAATCAA
1 GCTTAAGACAAATCAA
34838 G
1 G
34839 TGGTGAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (16 bp):
GCTTAAGACAAATCAA
Found at i:38115 original size:124 final size:124
Alignment explanation
Indices: 37949--38172 Score: 299
Period size: 124 Copynumber: 1.8 Consensus size: 124
37939 TTATCCGAGT
* * * *
37949 TGAATATATACATACACATGTCAGGTTACCCGTCCGAGCTAAACCTTTAAATTGATATCA-AGTT
1 TGAAAATATACATACACATGTCAGGTTACCCGTCCGAGCTAAACCTTTAAACTAACATCAGA-TT
** * *
38013 ACCAGTCCTGGCTAAATCTATGTCACAAGTATCTTCAATACATAAATAACTCGTTCTAGC
65 ACCAGTCCAAGCTAAACCTATATCACAAGTATCTTCAATACATAAATAACTCGTTCTAGC
* * **
38073 TGAAAATATATATACACATGTCAGGTTACTCGTTTG-GCCTAAACCTTTAAACTAACATCAGATT
1 TGAAAATATACATACACATGTCAGGTTACCCGTCCGAG-CTAAACCTTTAAACTAACATCAGATT
*
38137 ACTAGTCCAAGCTAAACCTATATCACAAGTATCTTC
65 ACCAGTCCAAGCTAAACCTATATCACAAGTATCTTC
38173 GATATATCAA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
123 1 0.01
124 83 0.98
125 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (124 bp):
TGAAAATATACATACACATGTCAGGTTACCCGTCCGAGCTAAACCTTTAAACTAACATCAGATTA
CCAGTCCAAGCTAAACCTATATCACAAGTATCTTCAATACATAAATAACTCGTTCTAGC
Done.