Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000522.1 Kokia drynarioides strain JFW-HI SEQ_111411, 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: 16504
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:835 original size:98 final size:98
Alignment explanation
Indices: 669--1585 Score: 754
Period size: 98 Copynumber: 9.4 Consensus size: 98
659 TCGAAACTGT
*
669 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
* *
734 TTCATGTTTCTGAGGTACATGGTTTGCCGTTGT
66 TTCATGTTTCTGAGGTACATGGTTCGCCGTTGC
* *
767 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAATCGCCGTTACGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
* * * *
832 TTCATGTTTTTGAGGTACAAGGTTCGTCATTGC
66 TTCATGTTTCTGAGGTACATGGTTCGCCGTTGC
* * * * *
865 GACTTAAGCCTTTCCCTACATATCTTTGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
* * * * * *
930 CTCATGTTTTTAAGGTATAAGGTTCGTCGTTGC
66 TTCATGTTTCTGAGGTACATGGTTCGCCGTTGC
* * * * * *
963 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTTGTCATTGCGACTTAAATATTTCCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
* * **
1028 TTCATATCTTC-GTGGTAC-TGGATTTACCGTTGC
66 TTCATGT-TTCTGAGGTACATGG-TTCGCCGTTGC
** * * * * * * * * *
1061 -AGCTTAAGTCTTTCTCTTCATGT-TTCTGAGGTACAAGGTTCGCCATTGTGACTT-AATCTTTT
1 GA-CTTAAACCTTTCCCTCCATATCTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAATC-TTT
* * **
1123 CCCTCCATATCTTC--ATGGTAC-TGGATTCGATGTTGC
63 CCCTTCATGT-TTCTGA-GGTACATGG-TTCGCCGTTGC
* * * * * * *
1159 GACTTAAATCTTTCCCTTCATGT-TTCTGAGGT-GTA-ACGTTCACCGTTGCGACTTAAA-CATT
1 GACTTAAACCTTTCCCTCCATATCTTC-GTGGTACTAGA--TTCGCCGTTGCGGCTTAAATC-TT
* * * *
1220 TCCCTTCATATCTGC-GTGGTAC-TAGATTCGCCGTTGC
62 TCCCTTCATGT-TTCTGAGGTACAT-GGTTCGCCGTTGC
* * * * * * * * ** *
1257 GGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACAAGGTTCACCGTTGCAACTTAAACCTTTCC
1 GACTTAAACCTTTCCCTCCATATCTTC-GTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCC
* * * * *
1321 CTCCATATCTTC-GTGGTAC-TGGATTCGCCATTGT
65 CTTCATGT-TTCTGAGGTACATGG-TTCGCCGTTGC
* * * * * *
1355 GGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTGGATTTGTCGTTGCGG-TATAAATCTTTCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCT-TAAATCTTTCC
* *
1419 CTTCATGTTTCTGAGGTACAAGGTTCACCGTTGC
65 CTTCATGTTTCTGAGGTACATGGTTCGCCGTTGC
* * *
1453 GACTTAAACCTTTCCCTCTATATATTCGTGGTACTAGATTCGTCGTTGCGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
* * * *
1518 TTCAAGTTTCTGAAGTGCAAGGTTCGCCGTTGC
66 TTCATGTTTCTGAGGTACATGGTTCGCCGTTGC
*
1551 GACTTAAACCTTTACCTCCATATCTTCGTGGTACT
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACT
1586 GAAACCTGTA
Statistics
Matches: 685, Mismatches: 113, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
97 15 0.02
98 656 0.96
99 14 0.02
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (98 bp):
GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCC
TTCATGTTTCTGAGGTACATGGTTCGCCGTTGC
Found at i:969 original size:147 final size:147
Alignment explanation
Indices: 707--1563 Score: 629
Period size: 147 Copynumber: 5.8 Consensus size: 147
697 TGGTACTGGA
* * * * * * * *
707 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTACATGG-TTTGCCGTTGTGAC
1 TTCGTCGTTGCGACTTAAACCTTTCCCTTCATATCTTC-GTGGTAC-TGGATTCGCCGTTGCGGC
* * * * * ** * *
770 TTAAACCTTTCCCTCCATATCTTCGTGGTACT-AGAATCGCCGTTACGGCTTAAATCTTTCCCTT
64 TTAAATCTTTCCCTTCATGTTTTCGAGGTA-TAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTT
834 CATGTTTTTGAGGTACAAGG
128 CATGTTTTTGAGGTACAAGG
* * * * *
854 TTCGTCATTGCGACTTAAGCCTTTCCCTACATATCTTTGTGGTACTGGATTCGCCGTTACGGCTT
1 TTCGTCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTT
* ** * * *
919 AAATCTTTCCCCTCATGTTTTTAAGGTATAAGGTTCGTCGTTGCGACTTAAACCTTTCCCTCCAT
66 AAATCTTTCCCTTCATGTTTTCGAGGTATAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCAT
* * * * *
984 ATCTTCGTGGTAC-TGG
131 GTTTTTGAGGTACAAGG
* * ** ** *
1000 ATTTGTCATTGCGACTTAAATATTTCCCTTCATATCTTCGTGGTACTGGATTTACCGTTGCAGCT
1 -TTCGTCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCT
* * * * * *
1065 TAAGTCTTTCTCTTCATG-TTTCTGAGGTACAAGGTTCGCCATTGTGACTT-AATCTTTTCCCTC
65 TAAATCTTTCCCTTCATGTTTTC-GAGGTATAAGGTTCGCCGTTGCGACTTAAATC-TTTCCCTT
* * * *
1128 CAT-ATCTTCATGGTAC-TGG
128 CATGTTTTTGA-GGTACAAGG
* * * *
1147 ATTCGAT-GTTGCGACTTAAATCTTTCCCTTCATGT-TTCTGAGGTGTAAC--G-TTCACCGTTG
1 -TTCG-TCGTTGCGACTTAAACCTTTCCCTTCATATCTTC-G-TG-GT-ACTGGATTCGCCGTTG
* * * * * * *
1207 CGACTTAAA-CATTTCCCTTCATATCTGCGTGGTACT-AGATTCGCCGTTGCGGCTTAAATCTTT
60 CGGCTTAAATC-TTTCCCTTCATGTTTTCGAGGTA-TAAGGTTCGCCGTTGCGACTTAAATCTTT
*
1270 CCCTTCATGTTTCTGAGGTACAAGG
123 CCCTTCATGTTTTTGAGGTACAAGG
** * * * *
1295 TTCACCGTTGCAACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCATTGTGGCTT
1 TTCGTCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTT
* * * * * *
1360 AAATCTTTCCCTTCATATCTTCGTGGTACT--GGATTTGTCGTTGCG-GTATAAATCTTTCCCTT
66 AAATCTTTCCCTTCATGTTTTCGAGGTA-TAAGG-TTCGCCGTTGCGACT-TAAATCTTTCCCTT
*
1422 CATGTTTCTGAGGTACAAGG
128 CATGTTTTTGAGGTACAAGG
** * * *
1442 TTCACCGTTGCGACTTAAACCTTTCCC-TCTATATATTCGTGGTACTAGATTCGTCGTTGCGGCT
1 TTCGTCGTTGCGACTTAAACCTTTCCCTTC-ATATCTTCGTGGTACTGGATTCGCCGTTGCGGCT
* * ** *
1506 TAAATCTTTCCCTTCAAG-TTTCTGAAGTGCAAGGTTCGCCGTTGCGACTTAAACCTTT
65 TAAATCTTTCCCTTCATGTTTTC-GAGGTATAAGGTTCGCCGTTGCGACTTAAATCTTT
1564 ACCTCCATAT
Statistics
Matches: 561, Mismatches: 118, Indels: 62
0.76 0.16 0.08
Matches are distributed among these distances:
144 2 0.00
145 2 0.00
146 25 0.04
147 505 0.90
148 23 0.04
149 2 0.00
150 2 0.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (147 bp):
TTCGTCGTTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTGCGGCTT
AAATCTTTCCCTTCATGTTTTCGAGGTATAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCAT
GTTTTTGAGGTACAAGG
Found at i:1116 original size:245 final size:245
Alignment explanation
Indices: 711--1521 Score: 916
Period size: 245 Copynumber: 3.3 Consensus size: 245
701 ACTGGATTCG
* * * * * * * *
711 CCGTTGCGGCTTAAATCTTTCCCTTCATGT-TTCTGAGGTAC-ATGGTTTGCCGTTGTGACTTAA
1 CCGTTGCGACTTAAACCTTTCCCTCCATATCTTC-GTGGTACTA-GATTCGCCGTTGCGACTTAA
* * * * * * *
774 ACCTTTCCCTCCATATCTTCGTGGTACTAGAATCGCCGTTACGGCTTAAATCTTTCCCTTCATGT
64 ATCTTTCCCTTCATATCTTCGTGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGT
* * * * *
839 TTTTGAGGTACAAGGTTCGTCATTGCGACTTAAGCCTTTCCCTACATATCTTTGTGGTACTGGAT
129 TTCTGAGGTACAAGGTTCGCCATTGTGACTTAAACCTTTCCCTACATATCTTCGTGGTACTGGAT
* * * * * *
904 TCGCCGTTACGGCTTAAATCTTTCCCCTCATGTTTTTAAGGTATAAGGTTCG
194 TCGACGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCA
* * * * *
956 TCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTTGTCATTGCGACTTAAAT
1 CCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAAT
* * * *
1021 ATTTCCCTTCATATCTTCGTGGTACTGGATTTACCGTTGCAGCTTAAGTCTTTCTCTTCATGTTT
66 CTTTCCCTTCATATCTTCGTGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGTTT
* * * *
1086 CTGAGGTACAAGGTTCGCCATTGTGACTTAATCTTTTCCCTCCATATCTTCATGGTACTGGATTC
131 CTGAGGTACAAGGTTCGCCATTGTGACTTAAACCTTTCCCTACATATCTTCGTGGTACTGGATTC
* * * *
1151 GATGTTGCGACTTAAATCTTTCCCTTCATGTTTCTGAGGTGTAACGTTCA
196 GACGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCA
* * * *
1201 CCGTTGCGACTTAAACATTTCCCTTCATATCTGCGTGGTACTAGATTCGCCGTTGCGGCTTAAAT
1 CCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAAT
* * * * * * *
1266 CTTTCCCTTCATGT-TTCTGAGGTACAAGG-TTCACCGTTGCAACTTAAACCTTTCCCTCCATAT
66 CTTTCCCTTCATATCTTC-GTGGTAC-TGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGT
* * * * *
1329 CTTC-GTGGTAC-TGGATTCGCCATTGTGGCTTAAATCTTTCCCTTCATATCTTCGTGGTACTGG
129 -TTCTGAGGTACAAGG-TTCGCCATTGTGACTTAAACCTTTCCCTACATATCTTCGTGGTACTGG
* * *
1392 ATTTGTCGTTGCGG-TATAAATCTTTCCCTTCATGTTTCTGAGGTACAAGGTTCA
192 ATTCGACGTTGCGGCT-TAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCA
* * * *
1446 CCGTTGCGACTTAAACCTTTCCCTCTATATATTCGTGGTACTAGATTCGTCGTTGCGGCTTAAAT
1 CCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAAT
1511 CTTTCCCTTCA
66 CTTTCCCTTCA
1522 AGTTTCTGAA
Statistics
Matches: 478, Mismatches: 81, Indels: 14
0.83 0.14 0.02
Matches are distributed among these distances:
244 6 0.01
245 464 0.97
246 8 0.02
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (245 bp):
CCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGCGACTTAAAT
CTTTCCCTTCATATCTTCGTGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGTTT
CTGAGGTACAAGGTTCGCCATTGTGACTTAAACCTTTCCCTACATATCTTCGTGGTACTGGATTC
GACGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTGAGGTATAAGGTTCA
Found at i:2523 original size:13 final size:12
Alignment explanation
Indices: 2505--2534 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2495 CGACCTCTCC
2505 TTTTTCTTTTTCT
1 TTTTTCTTTTT-T
2518 TTTTTCTTTTTT
1 TTTTTCTTTTTT
2530 TTTTT
1 TTTTT
2535 GGTGAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:3383 original size:16 final size:17
Alignment explanation
Indices: 3362--3401 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
3352 TCATCATGAC
3362 TTTCTTTTTCTTCCT-T
1 TTTCTTTTTCTTCCTCT
*
3378 TTTC-TTTTCTTCTTCT
1 TTTCTTTTTCTTCCTCT
3394 TTTCTTTT
1 TTTCTTTT
3402 CTTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 9 0.43
17 3 0.14
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTCTTCCTCT
Found at i:3387 original size:5 final size:5
Alignment explanation
Indices: 3377--3434 Score: 68
Period size: 5 Copynumber: 11.8 Consensus size: 5
3367 TTTTCTTCCT
*
3377 TTTTC TTTTC TTCTTC TTTTC TTTTC TTTTC TTTT- TTATT- TTTTA TTTT-
1 TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC
3426 TTTTC TTTT
1 TTTTC TTTT
3435 AAAAGATGCC
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.16
5 36 0.73
6 5 0.10
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:3388 original size:21 final size:21
Alignment explanation
Indices: 3362--3412 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3352 TCATCATGAC
3362 TTTCTTTTTCTTC-CTTTTTCT
1 TTTCTTTTTCTTCTC-TTTTCT
* *
3383 TTTCTTCTTCTTTTCTTTTCT
1 TTTCTTTTTCTTCTCTTTTCT
3404 TTTCTTTTT
1 TTTCTTTTT
3413 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTTTTCTTCTCTTTTCT
Found at i:3412 original size:16 final size:17
Alignment explanation
Indices: 3375--3434 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
3365 CTTTTTCTTC
*
3375 CTTTTTCTTTTCTTCTT
1 CTTTTTCTTTTCTTATT
3392 C-TTTTCTTTTCTT-TT
1 CTTTTTCTTTTCTTATT
*
3407 CTTTTT-TATTTTTTATT
1 CTTTTTCT-TTTCTTATT
*
3424 TTTTTTCTTTT
1 CTTTTTCTTTT
3435 AAAAGATGCC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 4 0.11
16 21 0.57
17 11 0.30
18 1 0.03
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTTTCTTTTCTTATT
Found at i:3481 original size:3 final size:3
Alignment explanation
Indices: 3473--3513 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3463 GGCCTTTTCT
* *
3473 TTC TTC TTC TTC TTC TTC TTC ATC ATC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3514 TTTTCTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:3841 original size:13 final size:13
Alignment explanation
Indices: 3823--3849 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3813 TCGTAGCAAA
3823 TTCGGAGACAAGT
1 TTCGGAGACAAGT
3836 TTCGGAGACAAGT
1 TTCGGAGACAAGT
3849 T
1 T
3850 ACATCCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (13 bp):
TTCGGAGACAAGT
Found at i:6766 original size:32 final size:32
Alignment explanation
Indices: 6730--6795 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
6720 TAGCAATAAT
** *
6730 ATTATCATGGTATTTCACAGAAAAAGCAAAGG
1 ATTATCATAATATTTAACAGAAAAAGCAAAGG
* *
6762 ATTATCATAATATTTAATAGAAAATGCAAAGG
1 ATTATCATAATATTTAACAGAAAAAGCAAAGG
6794 AT
1 AT
6796 CATATATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.29
Consensus pattern (32 bp):
ATTATCATAATATTTAACAGAAAAAGCAAAGG
Found at i:11191 original size:27 final size:27
Alignment explanation
Indices: 11142--11196 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
11132 AGTTGATAAA
11142 AATTTCTTTTGAACCCCTTAAAAATTG
1 AATTTCTTTTGAACCCCTTAAAAATTG
11169 AATTT-TTTTGAACCCCTTAAAAATTG
1 AATTTCTTTTGAACCCCTTAAAAATTG
11195 AA
1 AA
11197 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.40
Consensus pattern (27 bp):
AATTTCTTTTGAACCCCTTAAAAATTG
Found at i:15051 original size:17 final size:17
Alignment explanation
Indices: 15029--15062 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15019 TAAGTGGATG
*
15029 TCTAACTCCTTTAAACC
1 TCTAACTCATTTAAACC
15046 TCTAACTCATTTAAACC
1 TCTAACTCATTTAAACC
15063 CTCGTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (17 bp):
TCTAACTCATTTAAACC
Done.