Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004849.1 Kokia drynarioides strain JFW-HI SEQ_118508, 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: 29791
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:1269 original size:41 final size:41
Alignment explanation
Indices: 1222--1306 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
1212 GAATTTATTA
1222 ATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACC
1 ATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACC
*
1263 ATATAAAGCCAATTACAATCAATGTTAGCTACCCTACCACC
1 ATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACC
1304 ATA
1 ATA
1307 GTTGACACGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (41 bp):
ATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACC
Found at i:1370 original size:67 final size:67
Alignment explanation
Indices: 1262--1437 Score: 277
Period size: 67 Copynumber: 2.7 Consensus size: 67
1252 ACCCTACCAC
* *
1262 CATATAAAGCCAATTACAATCAATGTTAGCTACCCTACCACCATAGTTGACACGTAACAACCGAT
1 CATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACCATAGTTGACACGTAACAACCGAC
1327 AA
66 AA
*
1329 CATATAAAGCCAATTACAATCAATGTCAGCTTCCCTACCACCATAGTTGACACGTAACAACCGAC
1 CATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACCATAGTTGACACGTAACAACCGAC
1394 AA
66 AA
* * *
1396 CATATAAAGCAAATT---ATTAATGGCAGCTACCCTACCACCATA
1 CATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACCATA
1438 TAAAGCCAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
64 24 0.24
67 78 0.76
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (67 bp):
CATATAAAGCCAATTACAATCAATGTCAGCTACCCTACCACCATAGTTGACACGTAACAACCGAC
AA
Found at i:1469 original size:41 final size:41
Alignment explanation
Indices: 1414--1519 Score: 194
Period size: 41 Copynumber: 2.6 Consensus size: 41
1404 GCAAATTATT
*
1414 AATGGCAGCTACCCTACCACCATATAAAGCCAAGTACAATC
1 AATGTCAGCTACCCTACCACCATATAAAGCCAAGTACAATC
1455 AATGTCAGCTACCCTACCACCATATAAAGCCAAGTACAATC
1 AATGTCAGCTACCCTACCACCATATAAAGCCAAGTACAATC
*
1496 AATGTCAGGTACCCTACCACCATA
1 AATGTCAGCTACCCTACCACCATA
1520 GTTGACACGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.38, C:0.32, G:0.11, T:0.19
Consensus pattern (41 bp):
AATGTCAGCTACCCTACCACCATATAAAGCCAAGTACAATC
Found at i:2741 original size:25 final size:23
Alignment explanation
Indices: 2700--2745 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2690 ATAATTAGGG
2700 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
2723 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
2746 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:6797 original size:26 final size:26
Alignment explanation
Indices: 6757--6813 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
6747 TATTTTTGCT
6757 TATTTATTATCATTTGATATCTAATAA
1 TATTTATTATCATTTGATAT-TAATAA
* *
6784 TATTT-TTATTATTTGATATTAATAG
1 TATTTATTATCATTTGATATTAATAA
6809 TATTT
1 TATTT
6814 GTTTTCCGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.36
26 13 0.46
27 5 0.18
ACGTcount: A:0.33, C:0.04, G:0.05, T:0.58
Consensus pattern (26 bp):
TATTTATTATCATTTGATATTAATAA
Found at i:7570 original size:10 final size:11
Alignment explanation
Indices: 7546--7574 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
7536 AACTTTTGAT
7546 TTTAAATTAGG
1 TTTAAATTAGG
7557 TTTAAATT-GG
1 TTTAAATTAGG
7567 TTTAAATT
1 TTTAAATT
7575 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (11 bp):
TTTAAATTAGG
Found at i:7602 original size:20 final size:18
Alignment explanation
Indices: 7567--7617 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
7557 TTTAAATTGG
7567 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
7585 TTTAAATTTATCTTTTTAAA
1 TTTAAATTTA--TTTTTAAA
* *
7605 TTTGAATTGATTT
1 TTTAAATTTATTT
7618 AAAAACTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 13 0.45
20 16 0.55
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:8408 original size:6 final size:6
Alignment explanation
Indices: 8399--8457 Score: 55
Period size: 6 Copynumber: 9.5 Consensus size: 6
8389 TGGTAATAAA
* * * * *
8399 TAATAT TAATAAT TATTAA TAAAAA TATTAT TAATAT TAATAAT TAATAT
1 TAATAT TAAT-AT TAATAT TAATAT TAATAT TAATAT TAAT-AT TAATAT
8449 TAATAT TAA
1 TAATAT TAA
8458 ATAATAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 32 0.74
7 11 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TAATAT
Found at i:8408 original size:13 final size:13
Alignment explanation
Indices: 8380--8453 Score: 65
Period size: 13 Copynumber: 6.3 Consensus size: 13
8370 CGTTATTAAC
**
8380 AATAAATAATGGT
1 AATAAATAATATT
8393 AATAAATAATATT
1 AATAAATAATATT
8406 AAT-AAT--TATT
1 AATAAATAATATT
8416 AATAAA-AATATT
1 AATAAATAATATT
8428 -AT---TAATATT
1 AATAAATAATATT
*
8437 AATAATTAATATT
1 AATAAATAATATT
8450 AATA
1 AATA
8454 TTAAATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
9 6 0.12
10 9 0.18
11 4 0.08
12 7 0.14
13 25 0.49
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
AATAAATAATATT
Found at i:8465 original size:13 final size:12
Alignment explanation
Indices: 8355--8467 Score: 69
Period size: 12 Copynumber: 9.5 Consensus size: 12
8345 GGTTATATAT
8355 TAATAATATTAA
1 TAATAATATTAA
***
8367 TAACGTTATTAA
1 TAATAATATTAA
*
8379 CAATAAATAATGGTAA
1 TAAT-AAT-AT--TAA
8395 TAAATAATATTAA
1 T-AATAATATTAA
8408 TAAT--TATTAA
1 TAATAATATTAA
*
8418 TAAAAATATT-A
1 TAATAATATTAA
8429 T--TAATATTAA
1 TAATAATATTAA
8439 TAATTAATATTAA
1 TAA-TAATATTAA
*
8452 TATTAA-A-TAA
1 TAATAATATTAA
8462 TAATAA
1 TAATAA
8468 AAAATTGAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
9 6 0.08
10 19 0.24
11 3 0.04
12 21 0.27
13 16 0.21
14 2 0.03
15 2 0.03
16 6 0.08
17 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:8465 original size:19 final size:19
Alignment explanation
Indices: 8418--8466 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
8408 TAATTATTAA
*
8418 TAAA-AATATTATTAATAT
1 TAAATAATAATATTAATAT
8436 T-AATAATTAATATTAATAT
1 TAAATAA-TAATATTAATAT
8455 TAAATAATAATA
1 TAAATAATAATA
8467 AAAAATTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 3 0.11
19 17 0.63
20 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATAATAATATTAATAT
Found at i:9574 original size:29 final size:29
Alignment explanation
Indices: 9496--9751 Score: 94
Period size: 30 Copynumber: 8.8 Consensus size: 29
9486 AAGGTCCCTA
* *
9496 AACTGTCCAAAAATTACATTTTTACA-CG
1 AACTTTCCAAAAATTACATTTTAACATCG
* *
9524 AACTTTCC-AAAATTCCTTTTTTAACATCG
1 AACTTTCCAAAAATTAC-ATTTTAACATCG
** * ** *
9553 ATTTTTCCAAAAATTACATTTTTACCCCTA
1 AACTTTCCAAAAATTACATTTTAACATC-G
* * *
9583 AACTTTCCAAAACTCTA-TTTTTAACCTCG
1 AACTTTCCAAAAAT-TACATTTTAACATCG
** * *
9612 ATTTTTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCCAAAAATTACA-TTTTAACATCG
* * * *
9642 AACCTTT-AAAAAATTCCATTTTTGACCTCG
1 AA-CTTTCCAAAAATTACA-TTTTAACATCG
* * ** *
9672 -ATTTGTCCAAAAATTACCATTTT-CCCCCC
1 AACTT-TCCAAAAATTA-CATTTTAACATCG
* * * **
9701 AAATTTCCAAAAATTCCATTTTACCCCCG
1 AACTTTCCAAAAATTACATTTTAACATCG
*
9730 AACATT-CAAAAATTACCATTTT
1 AACTTTCCAAAAATTA-CATTTT
9752 GCCCTCGGGT
Statistics
Matches: 172, Mismatches: 42, Indels: 27
0.71 0.17 0.11
Matches are distributed among these distances:
27 7 0.04
28 32 0.19
29 56 0.33
30 70 0.41
31 7 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (29 bp):
AACTTTCCAAAAATTACATTTTAACATCG
Found at i:9575 original size:30 final size:30
Alignment explanation
Indices: 9501--9694 Score: 143
Period size: 30 Copynumber: 6.6 Consensus size: 30
9491 CCCTAAACTG
* *
9501 TCCAAAAATTACATTTTT-A-CACGAACTT
1 TCCAAAAATTACATTTTTAACCTCGATCTT
* * * *
9529 TCC-AAAATTCCTTTTTTAACATCGATTTT
1 TCCAAAAATTACATTTTTAACCTCGATCTT
* * *
9558 TCCAAAAATTACATTTTT-ACCCCTAAACTT
1 TCCAAAAATTACATTTTTAACCTC-GATCTT
* *
9588 TCC-AAAACT-CTATTTTTAACCTCGATTTT
1 TCCAAAAATTAC-ATTTTTAACCTCGATCTT
* *
9617 TCCAAAAATTACATTTTTACCCTCGAACCTT
1 TCCAAAAATTACATTTTTAACCTCG-ATCTT
* * *
9648 T-AAAAAATTCCATTTTTGACCTCGAT-TT
1 TCCAAAAATTACATTTTTAACCTCGATCTT
9676 GTCCAAAAATTACCATTTT
1 -TCCAAAAATTA-CATTTT
9695 CCCCCCAAAT
Statistics
Matches: 125, Mismatches: 29, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
27 12 0.10
28 7 0.06
29 30 0.24
30 65 0.52
31 11 0.09
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (30 bp):
TCCAAAAATTACATTTTTAACCTCGATCTT
Found at i:9607 original size:59 final size:58
Alignment explanation
Indices: 9501--9722 Score: 252
Period size: 59 Copynumber: 3.8 Consensus size: 58
9491 CCCTAAACTG
* * *
9501 TCCAAAAATTACATTTTTA-CACGAACTTTCCAAAATTCCT-TTTTTAACATCGATTTT
1 TCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATT-CTATTTTTAACCTCGATTTT
*
9558 TCCAAAAATTACATTTTTACCCCTAAACTTTCCAAAACTCTATTTTTAACCTCGATTTT
1 TCCAAAAATTACATTTTTACCCC-AAACTTTCCAAAATTCTATTTTTAACCTCGATTTT
* ** * * *
9617 TCCAAAAATTACATTTTTACCCTCGAACCTTTAAAAAATTCCATTTTTGACCTCGATTTG
1 TCCAAAAATTACATTTTTACCC-C-AAACTTTCCAAAATTCTATTTTTAACCTCGATTTT
** *
9677 TCCAAAAATTACCATTTTCCCCCCAAA-TTTCCAAAAATTCCATTTT
1 TCCAAAAATTA-CATTTTTACCCCAAACTTTCC-AAAATTCTATTTT
9723 ACCCCCGAAC
Statistics
Matches: 142, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
57 19 0.13
58 7 0.05
59 66 0.46
60 41 0.29
61 9 0.06
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCCAAACTTTCCAAAATTCTATTTTTAACCTCGATTTT
Found at i:9721 original size:28 final size:30
Alignment explanation
Indices: 9677--9751 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
9667 CCTCGATTTG
9677 TCCAAAAATTACCATTTT-CCCCCCAA-ATT
1 TCCAAAAATTACCATTTTACCCCCCAACA-T
*
9706 TCCAAAAATT-CCATTTTACCCCCGAACAT
1 TCCAAAAATTACCATTTTACCCCCCAACAT
9735 T-CAAAAATTACCATTTT
1 TCCAAAAATTACCATTTT
9752 GCCCTCGGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
28 15 0.36
29 26 0.62
30 1 0.02
ACGTcount: A:0.36, C:0.31, G:0.01, T:0.32
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTACCCCCCAACAT
Found at i:9768 original size:29 final size:29
Alignment explanation
Indices: 9677--9771 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
9667 CCTCGATTTG
* * *
9677 TCCAAAAATTACCATTTTCCCCCCAAATT
1 TCCAAAAATTACCATTTTACCCCCGAATA
*
9706 TCCAAAAATT-CCATTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAATA
* * * **
9734 TTCAAAAATTACCATTTTGCCCTCGGGTA
1 TCCAAAAATTACCATTTTACCCCCGAATA
9763 TCCAAAAAT
1 TCCAAAAAT
9772 CTCATTTTCA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 23 0.43
29 31 0.57
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.29
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAATA
Found at i:17904 original size:12 final size:12
Alignment explanation
Indices: 17889--17913 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17879 AGAAAAAAAA
17889 AAAAACAGTAGC
1 AAAAACAGTAGC
17901 AAAAACAGTAGC
1 AAAAACAGTAGC
17913 A
1 A
17914 GAATTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAACAGTAGC
Found at i:22919 original size:3 final size:3
Alignment explanation
Indices: 22877--22901 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22867 TGCGTCCATT
22877 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
22902 GTGTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:26434 original size:25 final size:26
Alignment explanation
Indices: 26406--26459 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
26396 AATATTTAAG
26406 ATTAAAAATAATT-TA-ATTTTCGTAT
1 ATTAAAAAT-ATTATATATTTTCGTAT
**
26431 ATT-ATTATATTATATATTTTCGTAT
1 ATTAAAAATATTATATATTTTCGTAT
26456 ATTA
1 ATTA
26460 TTTAAATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 5 0.21
25 16 0.67
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (26 bp):
ATTAAAAATATTATATATTTTCGTAT
Done.