Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008900.1 Kokia drynarioides strain JFW-HI SEQ_123588, 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: 2204
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Found at i:870 original size:28 final size:29
Alignment explanation
Indices: 829--902 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 29
819 AACGGAGTAA
* * *
829 AAAATGAGATTTTTGGATG-CCCGGGGGT
1 AAAATGATAATTTTGGAAGACCCGGGGGT
* **
857 AAAATGATAATTTTTGAAGATTCGGGGGT
1 AAAATGATAATTTTGGAAGACCCGGGGGT
886 AAAAT-AGTAATTTTGGA
1 AAAATGA-TAATTTTGGA
903 CACTTCAGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGATAATTTTGGAAGACCCGGGGGT
Found at i:882 original size:29 final size:28
Alignment explanation
Indices: 850--1274 Score: 147
Period size: 29 Copynumber: 14.7 Consensus size: 28
840 TTTGGATGCC
850 CGGGGGTAAAATGATAATTTTTGAAGATT
1 CGGGGGTAAAATG-TAATTTTTGAAGATT
* *
879 CGGGGGTAAAATAGTAATTTTGGACA-CTT
1 CGGGGGTAAAAT-GTAATTTTTGA-AGATT
* * * * * * *
908 CAGCGGCAAAATGGTACTTCTT-AGACACT
1 CGGGGGTAAAAT-GTAATTTTTGA-AGATT
*
937 CGGGGGTAAGAATGCAATTTTTGGAAG-TT
1 CGGGGGTAA-AATGTAATTTTT-GAAGATT
** *
966 TAGGGGTAAAACAGTAATTTTTGGAAG-TT
1 CGGGGGTAAAA-TGTAATTTTT-GAAGATT
* * * *
995 TGGGAGTAAAATGGTAATTTTCAGAAAATT
1 CGGGGGTAAAAT-GTAATTTT-TGAAGATT
* * *
1025 C-AGAGTCAAAAATG-ATATTTTTGAAAATT
1 CGGGGGT--AAAATGTA-ATTTTTGAAGATT
*** *
1054 AAAGGGTAAAATGGTAATTTTTTAA-AGTT
1 CGGGGGTAAAAT-GTAATTTTTGAAGA-TT
* * *
1083 TGGGGGCAAAAATGTGATTTTTTGGAAG-TT
1 CGGGGG-TAAAATGT-AATTTTT-GAAGATT
* *
1113 TGGGGGTAAAATGCAATTTTTGAA-AGTT
1 CGGGGGTAAAATGTAATTTTTGAAGA-TT
* *
1141 CGAGAGTAAAATGTAATTTTTGGAAG-TT
1 CGGGGGTAAAATGTAATTTTT-GAAGATT
*
1169 CAGGGGT-AAATGGTAATTTTTGGAAG-TT
1 CGGGGGTAAAAT-GTAATTTTT-GAAGATT
** * *
1197 CAAGGGTAAAATTGCAATTTTTAGAAAATT
1 CGGGGGTAAAA-TGTAATTTTT-GAAGATT
*** *
1227 AATGGGTAAAATGTAATTTTGTGAAGTTT
1 CGGGGGTAAAATGTAATTTT-TGAAGATT
* *
1256 AGGGGTTAAAATGT-ATTTT
1 CGGGGGTAAAATGTAATTTT
1275 AGAAAAGTTT
Statistics
Matches: 303, Mismatches: 63, Indels: 61
0.71 0.15 0.14
Matches are distributed among these distances:
27 7 0.02
28 68 0.22
29 169 0.56
30 51 0.17
31 8 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (28 bp):
CGGGGGTAAAATGTAATTTTTGAAGATT
Found at i:1014 original size:58 final size:57
Alignment explanation
Indices: 939--1274 Score: 194
Period size: 58 Copynumber: 5.8 Consensus size: 57
929 TAGACACTCG
* *
939 GGGGTAAGAAT-GCAATTTTTGGAAGTTTAGGGGTAAAACAGTAATTTTTGGAAGTT-T
1 GGGGTAA-AATGGTAATTTTTGAAAGTTTAGGGGTAAAA-AGTAATTTTTGGAAGTTAT
* * * * * * *
996 GGGAGTAAAATGGTAATTTTCAGAAAATTCA-GAGTCAAAAA-TGATATTTTTGAAAATTAA
1 GGG-GTAAAATGGTAATTTT-TGAAAGTTTAGGGGT-AAAAAGT-A-ATTTTTGGAAGTTAT
* * * * *
1056 AGGGTAAAATGGTAATTTTTTAAAGTTTGGGGGCAAAAATGTGATTTTTTGGAAGTT-T
1 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAA-GT-AATTTTTGGAAGTTAT
* * * *
1114 GGGGGTAAAAT-GCAATTTTTGAAAG-TTCGAGAGTAAAATGTAATTTTTGGAAGTTCA-
1 -GGGGTAAAATGGTAATTTTTGAAAGTTTAG-GGGTAAAAAGTAATTTTTGGAAGTT-AT
* * * * * * *
1171 GGGGT-AAATGGTAATTTTTGGAAGTTCAAGGGTAAAATTGCAATTTTTAGAAAATTAAT
1 GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAA-AGTAATTTTT-GGAAGTT-AT
*
1230 -GGGTAAAAT-GTAATTTTGTG-AAGTTTAGGGGTTAAAATGT-ATTTT
1 GGGGTAAAATGGTAATTTT-TGAAAGTTTAGGGG-TAAAAAGTAATTTT
1275 AGAAAAGTTT
Statistics
Matches: 215, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
55 4 0.02
56 37 0.17
57 27 0.13
58 73 0.34
59 69 0.32
60 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTAGGGGTAAAAAGTAATTTTTGGAAGTTAT
Found at i:1095 original size:30 final size:28
Alignment explanation
Indices: 1061--1161 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
1051 ATTAAAGGGT
1061 AAAATGGTAATTTTTTAAAGTTTGGGGGCA
1 AAAAT-GTAATTTTTTAAAGTTTGGGGG-A
* * *
1091 AAAATGTGATTTTTTGGAAGTTTGGGGGT
1 AAAATGTAATTTTTT-AAAGTTTGGGGGA
* * * * * *
1120 AAAATGCAATTTTTGAAAGTTCGAGAGT
1 AAAATGTAATTTTTTAAAGTTTGGGGGA
1148 AAAATGTAATTTTT
1 AAAATGTAATTTTT
1162 GGAAGTTCAG
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 22 0.37
29 21 0.36
30 16 0.27
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (28 bp):
AAAATGTAATTTTTTAAAGTTTGGGGGA
Found at i:1274 original size:86 final size:82
Alignment explanation
Indices: 940--1274 Score: 257
Period size: 86 Copynumber: 3.9 Consensus size: 82
930 AGACACTCGG
** * *
940 GGGTAAGAATGCAATTTTTGGAAGTTTAGGGGTAAAACAGTAATTTTTGGAAGTTT-GGGAGTAA
1 GGGTAA-AATGCAATTTTT-GAAAATTAAGGGTAAAA-TGTAATTTTT-GAAGTTTAGGG-GTAA
* * *
1004 AATGGTAATTTTCAGAAAATTC-A
61 AAT-GTAATTTT-TGGAAGTTCAA
* * * *
1027 GAGTCAAAAATG-ATATTTTTGAAAATTAAAGGGTAAAATGGTAATTTTTTAAAGTTTGGGGGCA
1 GGGT--AAAATGCA-ATTTTTGAAAATT-AAGGGTAAAAT-GTAA-TTTTTGAAGTTTAGGGG-T
* ***
1091 AAAATGTGATTTTTTGGAAGTTTGG
59 AAAATGT-AATTTTTGGAAGTTCAA
* * * *
1116 GGGTAAAATGCAATTTTTGAAAGTTCGAGAGTAAAATGTAATTTTTGGAAGTTCAGGGGT-AAAT
1 GGGTAAAATGCAATTTTTGAAAATT-AAGGGTAAAATGTAATTTTT-GAAGTTTAGGGGTAAAAT
1180 GGTAATTTTTGGAAGTTCAA
64 -GTAATTTTTGGAAGTTCAA
1200 GGGTAAAATTGCAATTTTTAGAAAATTAATGGGTAAAATGTAATTTTGTGAAGTTTAGGGGTTAA
1 GGGTAAAA-TGCAATTTTT-GAAAATTAA-GGGTAAAATGTAATTTT-TGAAGTTTAGGGG-TAA
1265 AATGT-ATTTT
61 AATGTAATTTT
1275 AGAAAAGTTT
Statistics
Matches: 199, Mismatches: 30, Indels: 39
0.74 0.11 0.15
Matches are distributed among these distances:
84 25 0.13
85 18 0.09
86 51 0.26
87 40 0.20
88 42 0.21
89 23 0.12
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (82 bp):
GGGTAAAATGCAATTTTTGAAAATTAAGGGTAAAATGTAATTTTTGAAGTTTAGGGGTAAAATGT
AATTTTTGGAAGTTCAA
Found at i:1282 original size:29 final size:30
Alignment explanation
Indices: 1147--1394 Score: 144
Period size: 30 Copynumber: 8.5 Consensus size: 30
1137 AGTTCGAGAG
* * *
1147 TAAAATGTAATTTTTG-GAAGTTCAGGGG-
1 TAAAATGTAATTTTAGAAAAGTTTAGGGGT
* * * *
1175 T-AAATGGTAATTTTTG-GAAGTTCAAGGG-
1 TAAAAT-GTAATTTTAGAAAAGTTTAGGGGT
* * *
1203 TAAAATTGCAATTTTTAGAAAA-TTAATGGG-
1 TAAAA-TGTAA-TTTTAGAAAAGTTTAGGGGT
**
1233 TAAAATGTAATTTT-GTGAAGTTTAGGGGT
1 TAAAATGTAATTTTAGAAAAGTTTAGGGGT
1262 TAAAATGT-ATTTTAGAAAAGTTTAGGGGT
1 TAAAATGTAATTTTAGAAAAGTTTAGGGGT
* * * *
1291 TAAAATATTATTTTCA-AAAAATTTAGAGGT
1 TAAAATGTAATTTT-AGAAAAGTTTAGGGGT
* *
1321 TAAAATATAATTTTCA-AAAAATTT-GAGGGT
1 TAAAATGTAATTTT-AGAAAAGTTTAG-GGGT
* *
1351 TAAAATATAATTTTTAG-AAAGTTTAAGGGT
1 TAAAATGTAA-TTTTAGAAAAGTTTAGGGGT
* *
1381 TAAAACGTGATTTT
1 TAAAATGTAATTTT
1395 TGGAAAATTC
Statistics
Matches: 183, Mismatches: 23, Indels: 27
0.79 0.10 0.12
Matches are distributed among these distances:
27 7 0.04
28 38 0.21
29 43 0.23
30 88 0.48
31 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
TAAAATGTAATTTTAGAAAAGTTTAGGGGT
Found at i:1316 original size:30 final size:30
Alignment explanation
Indices: 1253--1385 Score: 155
Period size: 30 Copynumber: 4.5 Consensus size: 30
1243 TTTTGTGAAG
* *
1253 TTTAGGGGTTAAAATGT-ATTTT-AGAAAAG
1 TTTAGGGGTTAAAATATAATTTTCA-AAAAA
*
1282 TTTAGGGGTTAAAATATTATTTTCAAAAAA
1 TTTAGGGGTTAAAATATAATTTTCAAAAAA
*
1312 TTTAGAGGTTAAAATATAATTTTCAAAAAA
1 TTTAGGGGTTAAAATATAATTTTCAAAAAA
* * *
1342 TTT-GAGGGTTAAAATATAATTTTTAGAAAG
1 TTTAG-GGGTTAAAATATAATTTTCAAAAAA
*
1372 TTTAAGGGTTAAAA
1 TTTAGGGGTTAAAA
1386 CGTGATTTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
29 17 0.19
30 73 0.80
31 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (30 bp):
TTTAGGGGTTAAAATATAATTTTCAAAAAA
Found at i:1395 original size:30 final size:30
Alignment explanation
Indices: 1182--1385 Score: 149
Period size: 30 Copynumber: 6.9 Consensus size: 30
1172 GGGTAAATGG
* *
1182 TAATTTTT-GGAAGTTCAAGGG-TAAAAT-
1 TAATTTTTAGAAAGTTTAAGGGTTAAAATA
* *
1209 TGCAATTTTTAGAAA-ATTAATGGG-TAAAATG
1 T--AATTTTTAGAAAGTTTAA-GGGTTAAAATA
* *
1240 TAATTTTGT-G-AAGTTTAGGGGTTAAAATG
1 TAATTTT-TAGAAAGTTTAAGGGTTAAAATA
*
1269 T-A-TTTTAGAAAAGTTTAGGGGTTAAAATA
1 TAATTTTTAG-AAAGTTTAAGGGTTAAAATA
* * * *
1298 TTATTTTCAAAAAATTT-AGAGGTTAAAATA
1 TAATTTTTAGAAAGTTTAAG-GGTTAAAATA
* * * *
1328 TAATTTTCAAAAAATTTGAGGGTTAAAATA
1 TAATTTTTAGAAAGTTTAAGGGTTAAAATA
1358 TAATTTTTAGAAAGTTTAAGGGTTAAAA
1 TAATTTTTAGAAAGTTTAAGGGTTAAAA
1386 CGTGATTTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 5 0.03
28 6 0.04
29 48 0.33
30 80 0.54
31 7 0.05
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (30 bp):
TAATTTTTAGAAAGTTTAAGGGTTAAAATA
Done.