Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004352.1 Kokia drynarioides strain JFW-HI SEQ_117693, 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, 984
Length: 1641
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Found at i:574 original size:20 final size:19
Alignment explanation
Indices: 528--573 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
518 TTAAAAATAA
528 AAATTTTTAAGAAAAGTTT
1 AAATTTTTAAGAAAAGTTT
547 AAATTTTTAA-ACAAAGTTT
1 AAATTTTTAAGA-AAAGTTT
*
566 TAATTTTT
1 AAATTTTT
574 TTTAACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (19 bp):
AAATTTTTAAGAAAAGTTT
Found at i:591 original size:132 final size:129
Alignment explanation
Indices: 426--767 Score: 436
Period size: 133 Copynumber: 2.6 Consensus size: 129
416 GATTTTGGGA
* * ** ** *
426 AAAGTTTTGGTTTTTTTTAAATAATTTCGAAATAAATTTTTTTTATTTTTAAGTAAAATAATGAT
1 AAAGTTTTGATTTTTTTTAACT-ATTTCGAAATAAA-AATTTGAATTTTTAAGTAAAATAGTGAT
491 TTTCTTTAAAAAAAAATGTTTAGATTTTTAAAAATAAAAA-TTTTTAAGAAAAGTT-TAAATTTT
64 TTTCTTTAAAAAAAAA--TTTAGATTTTT-AAAATAAAAATTTTTTAAGAAAAGTTCT-AATTTT
554 TAAAC
125 TAAAC
* * *
559 AAAGTTTTAATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTT
1 AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTT
* * *
624 TCTTTAAAAAAAAATTTAGATTTTTAAGATAAAAATTTGTTTTTTAGAAAAGTTCTGATTTTTAA
66 TCTTTAAAAAAAAATTTAGATTTTTAAAATAAAAA--T-TTTTTAAGAAAAGTTCTAATTTTTAA
689 AC
128 AC
* * *
691 AAAGTTTTGATTTTTTTAAAACTATTTTGTAATAAAAATTTGAATTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGATTTTTTT-TAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATT
756 TTCTTTAAAAAA
65 TTCTTTAAAAAA
768 GAGAAAGTTT
Statistics
Matches: 186, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
128 9 0.05
129 11 0.06
131 39 0.21
132 53 0.28
133 74 0.40
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (129 bp):
AAAGTTTTGATTTTTTTTAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTT
TCTTTAAAAAAAAATTTAGATTTTTAAAATAAAAATTTTTTAAGAAAAGTTCTAATTTTTAAAC
Found at i:649 original size:20 final size:19
Alignment explanation
Indices: 626--705 Score: 56
Period size: 19 Copynumber: 4.2 Consensus size: 19
616 AGTGATTTTC
626 TTTAAAAAAAAATTTAGATT
1 TTTAAAAAAAAATTT-GATT
*
646 TTTAAGATAAAAATTTG-TT
1 TTTAA-AAAAAAATTTGATT
* * *
665 TTT-TAGAAAAGTTCTGATT
1 TTTAAAAAAAAATT-TGATT
* **
684 TTTAAACAAAGTTTTGATT
1 TTTAAAAAAAAATTTGATT
703 TTT
1 TTT
706 TTAAAACTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 7 0.15
18 2 0.04
19 18 0.38
20 12 0.25
21 9 0.19
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (19 bp):
TTTAAAAAAAAATTTGATT
Found at i:747 original size:133 final size:130
Alignment explanation
Indices: 437--767 Score: 427
Period size: 132 Copynumber: 2.5 Consensus size: 130
427 AAGTTTTGGT
** ** *
437 TTTTTTTAAA-TAATTTCGAAATAAATTTTTTTTATTTTTAAGTAAAATAATGATTTTCTTTAAA
1 TTTTTTTAAACT-ATTTCGAAATAAA-AATTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAAA
501 AAAAAATGTTTAGATTTTTAAAAATAAAAATTTTTAAGAAAAGTTTAAATTTTTAAACAAAGTTT
64 AAAAAA-GTTTAGATTTTTAAAAATAAAAATTTTTAAGAAAAGTTTAAATTTTTAAACAAAGTTT
566 TAA
128 TAA
* * *
569 TTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAA
1 TTTTTTTAAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAAAAA
* * *
634 AAAA-TTTAGATTTTT-AAGATAAAAATTTGTTTTTTAGAAAAGTTCT-GATTTTTAAACAAAGT
66 AAAAGTTTAGATTTTTAAAAATAAAAA----TTTTTAAGAAAAGTT-TAAATTTTTAAACAAAGT
*
696 TTTGA
126 TTTAA
* *
701 TTTTTTTAAAACTATTTTGTAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAAAA
1 TTTTTTT-AAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAAAA
766 AA
65 AA
768 GAGAAAGTTT
Statistics
Matches: 177, Mismatches: 15, Indels: 13
0.86 0.07 0.06
Matches are distributed among these distances:
128 9 0.05
129 11 0.06
131 39 0.22
132 62 0.35
133 56 0.32
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (130 bp):
TTTTTTTAAACTATTTCGAAATAAAAATTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAAAAA
AAAAGTTTAGATTTTTAAAAATAAAAATTTTTAAGAAAAGTTTAAATTTTTAAACAAAGTTTTAA
Found at i:848 original size:150 final size:149
Alignment explanation
Indices: 681--1057 Score: 432
Period size: 150 Copynumber: 2.5 Consensus size: 149
671 AAAAGTTCTG
* * *
681 ATTTTTAAACAAAGTTTTGATTTTTTTAAAACTATTTTGTAATAAAA-ATTTGAATTTTTAAGTA
1 ATTTTTAAATAAAGTTTTGATTTTTTT--AACTATTTTGAAATAAAAGTTTTG-ATTTTTAAGTA
* ** * *
745 AAATAGTGATTTTCTTTAAA-AAAGAGAAAGTTTA-TATATATATTTTT-T-AAAATCTGTTTTT
63 AAATAGTGATTTTCATTAAAGAAA-AGAAAG-AAAGTATAGAT-TTTTTATAAAAATATGTTTTT
* *
806 TAGTTATTTTAAAGA-AAATTTTTAA
125 TAGTGATTTTAAAGAGAAA-GTTTAA
831 ATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGT--AA
1 ATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGTAAAA
*
894 -AGTGATTTTCATTAAAGAAAATAAAGAAAGTATAGATTTTTTAAAAATAAAAATATGTTTTTTA
66 TAGTGATTTTCATTAAAGAAAAGAAAGAAAGTATAGATTTTTT----ATAAAAATATGTTTTTTA
958 GTGATTTTAAAGAGAAAGTTTAA
127 GTGATTTTAAAGAGAAAGTTTAA
* *
981 ATTTTTAAATGAAGTTTTGATTTTTTTTTAACTATTTCT-AAATAAAAGTTTTGATTTTGAAGTA
1 ATTTTTAAATAAAGTTTTGA--TTTTTTTAACTATTT-TGAAATAAAAGTTTTGATTTTTAAGTA
*
1045 AAGTAGTGATTTT
63 AAATAGTGATTTT
1058 GTTTTAATCA
Statistics
Matches: 197, Mismatches: 14, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
144 6 0.03
145 26 0.13
146 5 0.03
148 27 0.14
149 5 0.03
150 76 0.39
151 3 0.02
152 38 0.19
153 1 0.01
154 1 0.01
155 9 0.05
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (149 bp):
ATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGTAAAA
TAGTGATTTTCATTAAAGAAAAGAAAGAAAGTATAGATTTTTTATAAAAATATGTTTTTTAGTGA
TTTTAAAGAGAAAGTTTAA
Found at i:866 original size:31 final size:30
Alignment explanation
Indices: 824--887 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
814 TTAAAGAAAA
*
824 TTTTTAAATTTTTAAAT-AAAGTTTTGATT
1 TTTTTAAATTTTGAAATAAAAGTTTTGATT
853 TTTTTAACTATTTTGAAATAAAAGTTTTGATT
1 TTTTTAA--ATTTTGAAATAAAAGTTTTGATT
885 TTT
1 TTT
888 AAGTAAAGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 7 0.23
31 9 0.29
32 15 0.48
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTTAAATTTTGAAATAAAAGTTTTGATT
Done.