Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007557.1 Kokia drynarioides strain JFW-HI SEQ_122185, 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: 35058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 17 characters in sequence are not A, C, G, or T
Found at i:949 original size:7 final size:7
Alignment explanation
Indices: 937--988 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
927 TTCAAAAAAA
937 GTCAACG
1 GTCAACG
944 GTCAACG
1 GTCAACG
* *
951 ATTAACG
1 GTCAACG
*
958 GTCAATG
1 GTCAACG
965 GTCAACG
1 GTCAACG
*
972 ATCAACG
1 GTCAACG
979 GTCAACG
1 GTCAACG
986 GTC
1 GTC
989 GATCAATGGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:967 original size:21 final size:21
Alignment explanation
Indices: 937--988 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
927 TTCAAAAAAA
*
937 GTCAACGGTCAACGATTAACG
1 GTCAACGGTCAACGATCAACG
*
958 GTCAATGGTCAACGATCAACG
1 GTCAACGGTCAACGATCAACG
979 GTCAACGGTC
1 GTCAACGGTC
989 GATCAATGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (21 bp):
GTCAACGGTCAACGATCAACG
Found at i:1052 original size:15 final size:15
Alignment explanation
Indices: 1032--1065 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1022 GGGTTTGGAC
1032 TTGGTTCAATTCGGT
1 TTGGTTCAATTCGGT
*
1047 TTGGTTCAATTGGGT
1 TTGGTTCAATTCGGT
1062 TTGG
1 TTGG
1066 GCTTAATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.32, T:0.47
Consensus pattern (15 bp):
TTGGTTCAATTCGGT
Found at i:2806 original size:30 final size:30
Alignment explanation
Indices: 2770--2937 Score: 121
Period size: 30 Copynumber: 5.7 Consensus size: 30
2760 CCATAGATAT
*
2770 CCACAAAGGCATCTCATATAACTGAATCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
2800 CCACAAAGGC-TCTCATATAACAT-ATTTC-A
1 CCACAAAGGCATCTCATATAAC-TGA-TTCAA
* * *
2829 CCACAAAGGTATCACATATAACAGATTCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
* * ** **
2859 CCACAAAGACTTAACATATAA-TGGATTCTG
1 CCACAAAGGCATCTCATATAACT-GATTCAA
* * * **
2889 CCACAAGGGCATCACTTATAACAAATTCAA
1 CCACAAAGGCATCTCATATAACTGATTCAA
* *
2919 CCACATAGGC-TTTCATATA
1 CCACAAAGGCATCTCATATA
2938 TCAAAATTAG
Statistics
Matches: 106, Mismatches: 25, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
29 31 0.29
30 75 0.71
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (30 bp):
CCACAAAGGCATCTCATATAACTGATTCAA
Found at i:2862 original size:59 final size:58
Alignment explanation
Indices: 2770--2937 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 58
2760 CCATAGATAT
* * * *
2770 CCACAAAGGCATCTCATATAACTGAATCAACCACAAAGGCTCTCATATAACATATT-TCA
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCT-TCATATAACAGATTCT-A
* * ** *
2829 CCACAAAGGTATCACATATAACAGATTCAACCACAAAGACTTAACATATAATGGATTCTG
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCTT--CATATAACAGATTCTA
* * * *
2889 CCACAAGGGCATCACTTATAACAAATTCAACCACATAGGCTTTCATATA
1 CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGC-TTCATATA
2938 TCAAAATTAG
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
58 1 0.01
59 42 0.47
60 44 0.49
61 3 0.03
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (58 bp):
CCACAAAGGCATCACATATAACAGATTCAACCACAAAGGCTTCATATAACAGATTCTA
Found at i:2942 original size:29 final size:28
Alignment explanation
Indices: 2905--2964 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
2895 GGGCATCACT
*
2905 TATAAC-AAATTCAACCACATAGGCTTTCA
1 TATAACAAAATT-AACCACAAAGGC-TTCA
* *
2934 TATATCAAAATTAGCCACAAAGGCTTCA
1 TATAACAAAATTAACCACAAAGGCTTCA
2962 TAT
1 TAT
2965 CGGTAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 15 0.56
30 5 0.19
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (28 bp):
TATAACAAAATTAACCACAAAGGCTTCA
Found at i:5396 original size:12 final size:12
Alignment explanation
Indices: 5379--5407 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5369 TTATTAATTC
5379 TATTTATTTTAA
1 TATTTATTTTAA
5391 TATTTATTTTAA
1 TATTTATTTTAA
5403 TATTT
1 TATTT
5408 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAA
Found at i:8387 original size:20 final size:20
Alignment explanation
Indices: 8339--8393 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
8329 TTATTTAAAA
* *
8339 CCCTGTATGCACTTCGATGC
1 CCCTGTATGCACTACGATAC
* * *
8359 CTCTATATGCACTACGGTAC
1 CCCTGTATGCACTACGATAC
8379 CCCTGTATGCACTAC
1 CCCTGTATGCACTAC
8394 AATGCCCTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (20 bp):
CCCTGTATGCACTACGATAC
Found at i:10887 original size:29 final size:29
Alignment explanation
Indices: 10854--10913 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
10844 TAGGAATAGG
*
10854 AAATTCCATTAGGATATCTTAGGTTAATT
1 AAATTCCATTAGGATATCTTAAGTTAATT
* * *
10883 AAATTCCATTAGGTTCTTTTAAGTTAATT
1 AAATTCCATTAGGATATCTTAAGTTAATT
10912 AA
1 AA
10914 TTTAATTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (29 bp):
AAATTCCATTAGGATATCTTAAGTTAATT
Found at i:11318 original size:15 final size:15
Alignment explanation
Indices: 11298--11326 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11288 GTGTGTTAAC
11298 TTTTAATTATTTTTA
1 TTTTAATTATTTTTA
11313 TTTTAATTATTTTT
1 TTTTAATTATTTTT
11327 GTTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTATTTTTA
Found at i:11322 original size:9 final size:9
Alignment explanation
Indices: 11298--11352 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
11288 GTGTGTTAAC
11298 TTTTAATTA
1 TTTTAATTA
11307 -TTT--TTA
1 TTTTAATTA
11313 TTTTAATTA
1 TTTTAATTA
**
11322 TTTTTGTTA
1 TTTTAATTA
11331 TTTTTAATTA
1 -TTTTAATTA
11341 -TTTAATTA
1 TTTTAATTA
11349 TTTT
1 TTTT
11353 TAGATACCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 11 0.30
9 13 0.35
10 7 0.19
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTTAATTA
Found at i:13122 original size:17 final size:17
Alignment explanation
Indices: 13097--13130 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13087 AAATCACCTC
*
13097 AATACCATATTATGCAA
1 AATACCATAATATGCAA
*
13114 AATATCATAATATGCAA
1 AATACCATAATATGCAA
13131 TAATTAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
AATACCATAATATGCAA
Found at i:14210 original size:23 final size:22
Alignment explanation
Indices: 14179--14225 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
14169 TCAAGTTTAA
*
14179 TATTATTATATTTATAAAATTTT
1 TATTATTATATTTA-AAAATATT
* *
14202 TATTTTTATTTTTAAAAATATT
1 TATTATTATATTTAAAAATATT
14224 TA
1 TA
14226 ATAATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATTATATTTAAAAATATT
Found at i:14376 original size:13 final size:14
Alignment explanation
Indices: 14360--14401 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
14350 TTTCAATTTT
14360 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
14373 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
14388 ATTTTAAATAATAT
1 ATTTT-AATAATAT
14402 TCTTCACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:14386 original size:16 final size:16
Alignment explanation
Indices: 14364--14400 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
14354 AATTTTATTT
14364 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
14381 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
14396 TAATA
1 TAATA
14401 TTCTTCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:16846 original size:21 final size:21
Alignment explanation
Indices: 16808--16847 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16798 GCTAAGCTGT
* **
16808 TTTAGGGTTTTAGTTTAGTAG
1 TTTAGGATTTTAAATTAGTAG
16829 TTTAGGATTTTAAATTAGT
1 TTTAGGATTTTAAATTAGT
16848 TCTATTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTAGGATTTTAAATTAGTAG
Found at i:26033 original size:20 final size:19
Alignment explanation
Indices: 26008--26057 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
25998 GTTGGGACAA
*
26008 TTTCTTT-TTCCTTCTCTTCT
1 TTTCTTTCTT-CTTCTATT-T
26028 TTTCTTTCTTCTTCTATTT
1 TTTCTTTCTTCTTCTATTT
26047 TTTC-TTCTTCT
1 TTTCTTTCTTCT
26058 GCCTTAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.25
19 5 0.18
20 14 0.50
21 2 0.07
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTTCTTCTTCTATTT
Found at i:26040 original size:15 final size:15
Alignment explanation
Indices: 26013--26057 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
26003 GACAATTTCT
*
26013 TTTTCCTTC-TCTTC
1 TTTTCTTTCTTCTTC
26027 TTTTCTTTCTTCTTC
1 TTTTCTTTCTTCTTC
26042 TATTT-TTTCTTCTTC
1 T-TTTCTTTCTTCTTC
26057 T
1 T
26058 GCCTTAAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 8 0.29
15 17 0.61
16 3 0.11
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCTTTCTTCTTC
Done.