Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011893.1 Kokia drynarioides strain JFW-HI SEQ_126890, 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: 26778
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:306 original size:80 final size:79
Alignment explanation
Indices: 208--365 Score: 262
Period size: 80 Copynumber: 2.0 Consensus size: 79
198 AGGAGAAATG
* * *
208 CCATGCCTTTTCAGCTACATCAGATCCTAATGAAGAGACATGACTCATTGGCTTTCCTACAAGAG
1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAG
273 TTAAAAATGAAATTC
66 TT-AAAATGAAATTC
* *
288 CCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTTATTAGCTTCCCTACAAGAG
1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAG
353 TTAAAATGAAATT
66 TTAAAATGAAATT
366 AGTGTTTGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 11 0.15
80 62 0.85
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (79 bp):
CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAG
TTAAAATGAAATTC
Found at i:3091 original size:50 final size:50
Alignment explanation
Indices: 2968--3131 Score: 244
Period size: 50 Copynumber: 3.3 Consensus size: 50
2958 CTTCATTAAG
* * * *
2968 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAA--GTG
1 TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
*
3016 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
1 TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
* *
3066 TTTTTTTTGTTAAATGCATCTTTGTTTTGTAATATGCATTATTAACT-AT
1 TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
3115 TTTTTTTTGTTAAATGC
1 TTTTTTTTGTTAAATGC
3132 CTTGCATTAA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
48 41 0.39
49 18 0.17
50 47 0.44
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (50 bp):
TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
Found at i:3673 original size:80 final size:79
Alignment explanation
Indices: 3575--3732 Score: 262
Period size: 80 Copynumber: 2.0 Consensus size: 79
3565 AGGAGAAATG
* * *
3575 CCATGCCTTTTCAGCTACATCAGATCCTAATGAAGAGACATGACTCATTGGCTTTCCTACAAGAG
1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAG
3640 TTAAAAATGAAATTC
66 TT-AAAATGAAATTC
* *
3655 CCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTTATTAGCTTCCCTACAAGAG
1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAG
3720 TTAAAATGAAATT
66 TTAAAATGAAATT
3733 AGTGTTTGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
79 11 0.15
80 62 0.85
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (79 bp):
CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCCTACAAGAG
TTAAAATGAAATTC
Found at i:6527 original size:6 final size:6
Alignment explanation
Indices: 6518--6566 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
6508 AGCATGAGGG
** * *
6518 AAAAGA AAAAGA AAGCGA AAAAGA AAAAAA TAAAAGA ACAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA
6567 GTTTGTGGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:9787 original size:50 final size:50
Alignment explanation
Indices: 9664--9827 Score: 244
Period size: 50 Copynumber: 3.3 Consensus size: 50
9654 CTTCATTAAG
* * * *
9664 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAA--GTG
1 TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
*
9712 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
1 TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
* *
9762 TTTTTTTTGTTAAATGCATCTTTGTTTTGTAATATGCATTATTAACT-AT
1 TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
9811 TTTTTTTTGTTAAATGC
1 TTTTTTTTGTTAAATGC
9828 CTTGCATTAA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
48 41 0.39
49 18 0.17
50 47 0.44
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (50 bp):
TTTTTTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTGTT
Found at i:12454 original size:62 final size:62
Alignment explanation
Indices: 12352--12469 Score: 200
Period size: 62 Copynumber: 1.9 Consensus size: 62
12342 GAAATGTGGT
*
12352 GGCTATATTTAGCAAGTAAATATCAGCCACACACATTGGTTGGTTGGCCATGCATATGAGGA
1 GGCTATATTTAGCAAGTAAATATCAGCCACACACAATGGTTGGTTGGCCATGCATATGAGGA
* **
12414 GGCTATATTTAGCAAGTAAATATCTGCCACACTTAATGGTTGGTTGGCCATGCATA
1 GGCTATATTTAGCAAGTAAATATCAGCCACACACAATGGTTGGTTGGCCATGCATA
12470 AGCACCTTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (62 bp):
GGCTATATTTAGCAAGTAAATATCAGCCACACACAATGGTTGGTTGGCCATGCATATGAGGA
Found at i:14260 original size:18 final size:18
Alignment explanation
Indices: 14226--14260 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14216 TCCTCATTGT
*
14226 TAAAAATAATAGAGAATG
1 TAAAAATAAAAGAGAATG
*
14244 TAAAAATAAAAGTGAAT
1 TAAAAATAAAAGAGAAT
14261 AAATACTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (18 bp):
TAAAAATAAAAGAGAATG
Found at i:16317 original size:10 final size:10
Alignment explanation
Indices: 16302--16336 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
16292 TGACATGGCT
*
16302 CGATGACTTC
1 CGATGACTGC
16312 CGATGACTGC
1 CGATGACTGC
16322 CGATGACTGC
1 CGATGACTGC
16332 CGATG
1 CGATG
16337 GTGGCTGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.23
Consensus pattern (10 bp):
CGATGACTGC
Found at i:22980 original size:94 final size:94
Alignment explanation
Indices: 22859--23309 Score: 668
Period size: 94 Copynumber: 4.8 Consensus size: 94
22849 TTACAGGCCA
* * * * * *
22859 TATCAATGGCTAAGGTATCGCATATGTTGCGAGCCCTCATCAGCTTAGTGTGAGCAGCATCGTTT
1 TATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCATCAGCTTAGTGTGAGCAGCATCGTAT
*
22924 ACTGGTAACAATTATATGTACAGATATCG
66 ACTGGTAACAATTATATGTACAGATACCG
* * *
22953 TATCGATGGCTGAGGTACCGCATATGTTACGGGTCCTCATTAGCTTATTGTGAGCAGCATCGTAT
1 TATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCATCAGCTTAGTGTGAGCAGCATCGTAT
*
23018 ACTGGTAACAGTTATATGTACAGATACCG
66 ACTGGTAACAATTATATGTACAGATACCG
* * * *
23047 TATCAATAGCTGAGGTACCGCATATTTTACGAGTCCTCGTCAGCTTAGTGTGAGCAGCATCGTAT
1 TATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCATCAGCTTAGTGTGAGCAGCATCGTAT
* * *
23112 ACTAGTAACAATTATATGTACAAATACCA
66 ACTGGTAACAATTATATGTACAGATACCG
* * *
23141 TATCGATGGCTGAGGTACCGCATATGTTGCAAGTCCTTATCAGCTTAGTGTGAGCAGCATCGTAT
1 TATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCATCAGCTTAGTGTGAGCAGCATCGTAT
23206 ACTGGTAACAATTATATGTACAGATACCG
66 ACTGGTAACAATTATATGTACAGATACCG
* * * *
23235 TATCGATGGCTGAGGCACTGCATATGTTACGAGTCCTCATCAGCTTAGTATGAGCAGCATCATAT
1 TATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCATCAGCTTAGTGTGAGCAGCATCGTAT
*
23300 ACTGATAACA
66 ACTGGTAACA
23310 GAGACAATTT
Statistics
Matches: 317, Mismatches: 40, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 317 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (94 bp):
TATCGATGGCTGAGGTACCGCATATGTTACGAGTCCTCATCAGCTTAGTGTGAGCAGCATCGTAT
ACTGGTAACAATTATATGTACAGATACCG
Done.