Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006918.1 Kokia drynarioides strain JFW-HI SEQ_121521, 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: 11013
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:62 original size:23 final size:23
Alignment explanation
Indices: 32--76 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22 TCAAATTATA
32 CATTGTATCTAAAAAAAACCATC
1 CATTGTATCTAAAAAAAACCATC
* *
55 CATTGTATCTCAATAAAACCAT
1 CATTGTATCTAAAAAAAACCAT
77 TCATCTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.29
Consensus pattern (23 bp):
CATTGTATCTAAAAAAAACCATC
Found at i:3368 original size:9 final size:9
Alignment explanation
Indices: 3354--3552 Score: 125
Period size: 9 Copynumber: 22.3 Consensus size: 9
3344 AATCATACAA
3354 ACATAACAT
1 ACATAACAT
*
3363 ACATAATAT
1 ACATAACAT
* *
3372 ACATGATAT
1 ACATAACAT
3381 ACAT-ACA-
1 ACATAACAT
* *
3388 A-ATATGCAA
1 ACATA-ACAT
3397 ACATAACAT
1 ACATAACAT
*
3406 ACATAATAT
1 ACATAACAT
3415 ACATGTATACAT
1 ACA--TA-ACAT
*
3427 ACA-AATAT
1 ACATAACAT
3435 ACA-AACAT
1 ACATAACAT
3443 AACACT-A-A-
1 -ACA-TAACAT
*
3451 ACATAATAT
1 ACATAACAT
*
3460 ACATAATAT
1 ACATAACAT
*
3469 ACATAATAT
1 ACATAACAT
*
3478 ACATATCAT
1 ACATAACAT
3487 ACAT-ACA-
1 ACATAACAT
3494 A-ATATACAT
1 ACATA-ACAT
3503 ACATAACAGT
1 ACATAACA-T
3513 ACATAACAT
1 ACATAACAT
3522 ACATAATCAT
1 ACATAA-CAT
3532 ACATAATCAT
1 ACATAA-CAT
3542 ACAT-ACAT
1 ACATAACAT
3550 ACA
1 ACA
3553 CAAACAATAA
Statistics
Matches: 158, Mismatches: 13, Indels: 39
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.03
7 6 0.04
8 26 0.16
9 80 0.51
10 33 0.21
11 2 0.01
12 6 0.04
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (9 bp):
ACATAACAT
Found at i:3471 original size:106 final size:105
Alignment explanation
Indices: 3354--3558 Score: 283
Period size: 106 Copynumber: 1.9 Consensus size: 105
3344 AATCATACAA
* *
3354 ACATAACATACATAATATACATGAT-ATACATACAAATATGCAAACATAACA-TACATAATATAC
1 ACATAACATACATAATATACAT-ATCATACATACAAATATACAAACATAACAGTACATAACATAC
*
3417 ATGTATACATACA-AAT-ATACAAACATAACACTAAACATAATAT
65 AT-AAT-CATACATAATCATACAAACAT-ACAC-AAACATAATAT
* *
3460 ACATAATATACATAATATACATATCATACATACAAATATACATACATAACAGTACATAACATACA
1 ACATAACATACATAATATACATATCATACATACAAATATACAAACATAACAGTACATAACATACA
*
3525 TAATCATACATAATCATACATACATACACAAACA
66 TAATCATACATAATCATACAAACATACACAAACA
3559 ATAAAGAAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
105 13 0.15
106 54 0.61
107 22 0.25
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.25
Consensus pattern (105 bp):
ACATAACATACATAATATACATATCATACATACAAATATACAAACATAACAGTACATAACATACA
TAATCATACATAATCATACAAACATACACAAACATAATAT
Found at i:3534 original size:97 final size:96
Alignment explanation
Indices: 3352--3534 Score: 237
Period size: 97 Copynumber: 1.9 Consensus size: 96
3342 ACAATCATAC
* * * *
3352 AAACATAACATACATAATATACATGATATACATACAAATATGCAAACATAACATACATAATATAC
1 AAACATAACATACATAATATACATAATATACATACAAACATACAAACATAACATACATAACATAC
3417 ATGTATACATACAAATATACAAACATAACACT
66 A-GTATACATACAAATATACAAACATAACACT
* * *
3449 AAACATAATATACATAATATACATAATATACATATCATACATACAAATAT-ACATACATAACAGT
1 AAACATAACATACATAATATACATAATATACATA-CAAACATACAAACATAACATACATAACA-T
3513 ACA-TA-ACATACATAATCATACA
64 ACAGTATACATACA-AAT-ATACA
3535 TAATCATACA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
95 7 0.09
96 5 0.07
97 48 0.64
98 15 0.20
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (96 bp):
AAACATAACATACATAATATACATAATATACATACAAACATACAAACATAACATACATAACATAC
AGTATACATACAAATATACAAACATAACACT
Found at i:3702 original size:37 final size:37
Alignment explanation
Indices: 3656--3726 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
3646 CAACAAAAAC
*
3656 AAAAAATAAAAGTTAGATATAATACCAATTAAAAATT
1 AAAAAATAAAAGTTAGATATAATACCAAATAAAAATT
* *
3693 AAAAAATAAAAGTTATATATAATACGAAATAAAA
1 AAAAAATAAAAGTTAGATATAATACCAAATAAAA
3727 CAGAGTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (37 bp):
AAAAAATAAAAGTTAGATATAATACCAAATAAAAATT
Found at i:3787 original size:32 final size:33
Alignment explanation
Indices: 3723--3853 Score: 228
Period size: 33 Copynumber: 4.0 Consensus size: 33
3713 AATACGAAAT
*
3723 AAAACAGAGTCAAAACCCAGAAAATAATAAAAC
1 AAAACAGAGTCAAAACCCAGAAAATAACAAAAC
3756 AAAACAGAGTCAAAACCCA-AAAATAACAAAAC
1 AAAACAGAGTCAAAACCCAGAAAATAACAAAAC
3788 AAAACAGAGTCAAAACCCAGAAAATAACAAAAC
1 AAAACAGAGTCAAAACCCAGAAAATAACAAAAC
* *
3821 AAAACAGAGTCAAAATCCAGAAAATAAAAAAAC
1 AAAACAGAGTCAAAACCCAGAAAATAACAAAAC
3854 CTCATCGACG
Statistics
Matches: 94, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 31 0.33
33 63 0.67
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.08
Consensus pattern (33 bp):
AAAACAGAGTCAAAACCCAGAAAATAACAAAAC
Found at i:3798 original size:65 final size:66
Alignment explanation
Indices: 3723--3853 Score: 228
Period size: 65 Copynumber: 2.0 Consensus size: 66
3713 AATACGAAAT
* *
3723 AAAACAGAGTCAAAACCCAGAAAATAATAAAACAAAACAGAGTCAAAACCCA-AAAATAACAAAA
1 AAAACAGAGTCAAAACCCAGAAAATAACAAAACAAAACAGAGTCAAAACCCAGAAAATAAAAAAA
3787 C
66 C
*
3788 AAAACAGAGTCAAAACCCAGAAAATAACAAAACAAAACAGAGTCAAAATCCAGAAAATAAAAAAA
1 AAAACAGAGTCAAAACCCAGAAAATAACAAAACAAAACAGAGTCAAAACCCAGAAAATAAAAAAA
3853 C
66 C
3854 CTCATCGACG
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 50 0.81
66 12 0.19
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.08
Consensus pattern (66 bp):
AAAACAGAGTCAAAACCCAGAAAATAACAAAACAAAACAGAGTCAAAACCCAGAAAATAAAAAAA
C
Found at i:6489 original size:58 final size:59
Alignment explanation
Indices: 6401--6621 Score: 220
Period size: 58 Copynumber: 3.8 Consensus size: 59
6391 GTTCATGGTT
* * * *
6401 AAAAATGGAATTTTT-AAACATTCGGGGGTAAAAAGGTAA-TTTTGAGAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAA-GTTCGAGGGTAAAAATGTAATTTTTGAGAGTTTCGAGGTC
* * * *
6459 AAAAATGGAAATTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTG-GAAGTTT-TAGGGTA
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAG-AGTTTCGA-GGTC
* * * * * * *
6518 AAAAAT-GAATTTTTAGAAGTTTGGGGGTAAAAATGAAATTTTTGAAAGTGTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAGTTTCGAGGTC
*
6576 AAAAATGGAATTTTTGGAAGTT-TAGGGGTAAAAATGTAATTTTTGA
1 AAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGTAATTTTTGA
6622 ATAGTTTAGG
Statistics
Matches: 132, Mismatches: 23, Indels: 15
0.78 0.14 0.09
Matches are distributed among these distances:
58 78 0.59
59 54 0.41
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAGTTTCGAGGTC
Found at i:6605 original size:59 final size:59
Alignment explanation
Indices: 6425--6628 Score: 243
Period size: 59 Copynumber: 3.5 Consensus size: 59
6415 TAAACATTCG
* * * * * *
6425 GGGGTAAAAAGGTAA-TTTTGAGAGTTTCGAGGTCAAAAATGGAAATTTTGG-AGGTTC
1 GGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* ** * * *
6482 GAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTAAAAAAT-GAATTTTTAGAAGTTTG
1 G-GGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* *
6541 GGGGTAAAAATGAAATTTTTGAAAGTGTCGGGGTCAAAAATGGAATTTTTGGAAGTTTA
1 GGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTA
6600 GGGGTAAAAATGTAATTTTTGAATAGTTT
1 GGGGTAAAAATGTAATTTTTGAA-AGTTT
6629 AGGGACCTTC
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
57 1 0.01
58 55 0.45
59 61 0.50
60 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
GGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTA
Found at i:6619 original size:29 final size:29
Alignment explanation
Indices: 6425--6632 Score: 183
Period size: 29 Copynumber: 7.1 Consensus size: 29
6415 TAAACATTCG
* *
6425 GGGGTAAAAAGGTAA-TTTT-GAGAGTTTC
1 GGGGTAAAAATGTAATTTTTGGA-AGTTTA
* * * * *
6453 GAGGTCAAAAATGGAAATTTTGG-AGGTTC
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTA
6482 GAGGGTAAAAATGTAATTTTTGGAAGTTTTA
1 G-GGGTAAAAATGTAATTTTTGGAAG-TTTA
* *
6513 -GGGTAAAAAATG-AATTTTTAGAAGTTTG
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTA
* * * *
6541 GGGGTAAAAATGAAATTTTTGAAAGTGTC
1 GGGGTAAAAATGTAATTTTTGGAAGTTTA
*
6570 GGGGTCAAAAATGGAATTTTTGGAAGTTTA
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTA
*
6600 GGGGTAAAAATGTAATTTTTGAATAGTTTA
1 GGGGTAAAAATGTAATTTTTGGA-AGTTTA
6630 GGG
1 GGG
6633 ACCTTCACGA
Statistics
Matches: 148, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
28 14 0.09
29 81 0.55
30 50 0.34
31 3 0.02
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:6628 original size:30 final size:29
Alignment explanation
Indices: 6371--6632 Score: 176
Period size: 29 Copynumber: 8.9 Consensus size: 29
6361 TCTCGAAGGC
* * * *
6371 AAAATGGTAATTTTGGGAAAGTTCATGGTTA
1 AAAAT-GTAATTTT-TGAAAGTTTAGGGGTA
* * **
6402 AAAATGGAATTTTT-AAACATTCGGGGGTA
1 AAAATGTAATTTTTGAAA-GTTTAGGGGTA
* * * *
6431 AAAAGGTAA-TTTTGAGAGTTTCGAGGTCA
1 AAAATGTAATTTTTGAAAGTTTAGGGGT-A
* * * * *
6460 AAAATGGAAATTTTG-GAGGTTCGAGGGTA
1 AAAATGTAATTTTTGAAAGTTTAG-GGGTA
*
6489 AAAATGTAATTTTTGGAAGTTTTA-GGGTAA
1 AAAATGTAATTTTTGAAAG-TTTAGGGGT-A
*
6519 AAAATG-AATTTTT-AGAAGTTTGGGGGTA
1 AAAATGTAATTTTTGA-AAGTTTAGGGGTA
* * *
6547 AAAATGAAATTTTTGAAAGTGTCGGGGTCA
1 AAAATGTAATTTTTGAAAGTTTAGGGGT-A
* *
6577 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGAAAGTTTAGGGGTA
6606 AAAATGTAATTTTTGAATAGTTTAGGG
1 AAAATGTAATTTTTGAA-AGTTTAGGG
6633 ACCTTCACGA
Statistics
Matches: 185, Mismatches: 32, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
28 23 0.12
29 96 0.52
30 59 0.32
31 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTAGGGGTA
Found at i:7755 original size:3 final size:3
Alignment explanation
Indices: 7747--7798 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
7737 TTATTGATAT
* * * * *
7747 TTA TTA TTA ATA ATA TTA TTA TTA TTG TTA TTTA TTA TAA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
7793 TTA TTA
1 TTA TTA
7799 ATGTCATTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:7772 original size:31 final size:31
Alignment explanation
Indices: 7736--7798 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
7726 TCCTTTTTCG
7736 ATTATTGATATTTATTATTAA-TAATATTATT
1 ATTATTGATATTTATTA-TAATTAATATTATT
*
7767 ATTATTGTTATTTATTATAATTAATATTATT
1 ATTATTGATATTTATTATAATTAATATTATT
7798 A
1 A
7799 ATGTCATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
ATTATTGATATTTATTATAATTAATATTATT
Found at i:10559 original size:24 final size:26
Alignment explanation
Indices: 10531--10580 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
10521 ATTTGATCCT
*
10531 TAAC-TTCTTTTTTTAATA-AAATTC
1 TAACTTTCTTTATTTAATAGAAATTC
*
10555 TAACTTTCTTTATTTGATAGAAATTC
1 TAACTTTCTTTATTTAATAGAAATTC
10581 ACCAGATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (26 bp):
TAACTTTCTTTATTTAATAGAAATTC
Done.