Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010613.1 Kokia drynarioides strain JFW-HI SEQ_125546, 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: 15236
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Found at i:86 original size:7 final size:7
Alignment explanation
Indices: 74--99 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
64 AATATTTATT
74 AATAATA
1 AATAATA
81 AATAATA
1 AATAATA
88 AATAATA
1 AATAATA
95 AATAA
1 AATAA
100 AAACGAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:273 original size:22 final size:23
Alignment explanation
Indices: 248--290 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
238 AAGTTAAATA
248 AAACGGTTTTCAA-AAAAAGGGG
1 AAACGGTTTTCAACAAAAAGGGG
* *
270 AAACGTTTTTTAACAAAAAGG
1 AAACGGTTTTCAACAAAAAGG
291 AGGATTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.23
Consensus pattern (23 bp):
AAACGGTTTTCAACAAAAAGGGG
Found at i:1115 original size:30 final size:30
Alignment explanation
Indices: 1080--1460 Score: 265
Period size: 30 Copynumber: 13.2 Consensus size: 30
1070 CTAAATTATT
* * *
1080 CAAAAATCCCATTTTTAACCTCGAAGCTTT
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
* * * **
1110 TAAAAATCTCAATTTTAACCCTAAAACTTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
* * *
1140 CAAAAATTCCATTTTT-ACCCCCAAACTAC
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
*
1169 CAAAAATCCCATTTTTAACCCCGAAGCATT-
1 CAAAAATCCCATTTTTAACCCCGAAAC-TTC
* * *
1199 CAAAAATTCTAATTTTAA--CC----C-T-
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
** * *
1221 -AAAAATTTCATTTTT-ACCCCCAAACTAC
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
*
1249 CAAAAATCCCATTTTTAACCCC-AAAGCTTT
1 CAAAAATCCCATTTTTAACCCCGAAA-CTTC
* * * **
1279 CAAAAATTCTAATTTTAACCCTAAAACTTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
* *
1309 CAAAAATTCCA-TTTT-ACCCTCG-AACTAC
1 CAAAAATCCCATTTTTAACCC-CGAAACTTC
* *
1337 CAAAAATCCCATTTTTAACCCCGAAGCTTT
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
* * *
1367 CAAAAATTCCATTTTTACCCCCG-AACCTC
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
* * *
1396 CAAAAATCCCATTTTTGACCCCAAAACTAC
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
* ** *
1426 CAAAAATCTCATTTTTAACCCTAAAACTTT
1 CAAAAATCCCATTTTTAACCCCGAAACTTC
1456 CAAAA
1 CAAAA
1461 GGTCCATTTT
Statistics
Matches: 273, Mismatches: 59, Indels: 38
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.00
21 12 0.04
22 3 0.01
24 1 0.00
26 1 0.00
28 21 0.08
29 73 0.27
30 157 0.58
31 4 0.01
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.30
Consensus pattern (30 bp):
CAAAAATCCCATTTTTAACCCCGAAACTTC
Found at i:1154 original size:29 final size:29
Alignment explanation
Indices: 1111--1509 Score: 216
Period size: 30 Copynumber: 13.8 Consensus size: 29
1101 CGAAGCTTTT
* *
1111 AAAAATCTCAATTTTAACCCTAAAACTTCC
1 AAAAAT-TCCATTTTAACCCCAAAACTTCC
* * *
1141 AAAAATTCCATTTTTACCCCCAAACTACC
1 AAAAATTCCATTTTAACCCCAAAACTTCC
* * *
1170 AAAAATCCCATTTTTAACCCCGAAGCATT-C
1 AAAAATTCCA-TTTTAACCCCAAAAC-TTCC
*
1200 AAAAATTCTAATTTTAA--CC----C-T--
1 AAAAATTC-CATTTTAACCCCAAAACTTCC
* * * *
1221 AAAAATTTCATTTTTACCCCCAAACTACC
1 AAAAATTCCATTTTAACCCCAAAACTTCC
* * *
1250 AAAAATCCCATTTTTAACCCCAAAGCTTTC
1 AAAAATTCCA-TTTTAACCCCAAAACTTCC
* *
1280 AAAAATTCTAATTTTAACCCTAAAACTTCC
1 AAAAATTC-CATTTTAACCCCAAAACTTCC
* *
1310 AAAAATTCCATTTT-ACCCTC-GAACTACC
1 AAAAATTCCATTTTAACCC-CAAAACTTCC
* * * *
1338 AAAAATCCCATTTTTAACCCCGAAGCTTTC
1 AAAAATTCCA-TTTTAACCCCAAAACTTCC
* ** *
1368 AAAAATTCCATTTTTACCCCCGAACCTCC
1 AAAAATTCCATTTTAACCCCAAAACTTCC
* * *
1397 AAAAATCCCATTTTTGACCCCAAAACTACC
1 AAAAATTCCA-TTTTAACCCCAAAACTTCC
* *
1427 AAAAA-TCTCATTTTTAACCCTAAAACTTTC
1 AAAAATTC-CA-TTTTAACCCCAAAACTTCC
** * **
1457 AAAAGGTCCATTTT--GCCCACAAACTTTT
1 AAAAATTCCATTTTAACCCCA-AAACTTCC
* *
1485 AAAAATCCCATTTTTGACCCCAAAA
1 AAAAATTCCA-TTTTAACCCCAAAA
1510 TTACCATTTC
Statistics
Matches: 281, Mismatches: 63, Indels: 50
0.71 0.16 0.13
Matches are distributed among these distances:
20 6 0.02
21 7 0.02
22 3 0.01
24 1 0.00
26 1 0.00
27 3 0.01
28 35 0.12
29 76 0.27
30 140 0.50
31 9 0.03
ACGTcount: A:0.38, C:0.29, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAATTCCATTTTAACCCCAAAACTTCC
Found at i:1337 original size:88 final size:87
Alignment explanation
Indices: 1221--1460 Score: 311
Period size: 88 Copynumber: 2.7 Consensus size: 87
1211 TTTTAACCCT
*
1221 AAAAATTTCATTTTTACCCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAAT
1 AAAAATTCCATTTTTA-CCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAAT
* *
1286 TCTAATTTTAACCCTAAAACTTCC
65 TC-AATTTTAACCCCAAAACCTCC
* *
1310 AAAAATTCCA-TTTTACCCTCGAACTACCAAAAATCCCATTTTTAACCCCGAAGCTTTCAAAAAT
1 AAAAATTCCATTTTTACCC-CAAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAAT
* * **
1374 TCCATTTTTACCCCCGAACCTCC
65 TCAATTTTAACCCCAAAACCTCC
* * * *
1397 AAAAATCCCATTTTTGACCCCAAAACTACCAAAAATCTCATTTTTAACCCTAAAACTTTCAAAA
1 AAAAATTCCATTTTT-ACCCC-AAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAA
1461 GGTCCATTTT
Statistics
Matches: 132, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
87 27 0.20
88 55 0.42
89 50 0.38
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.30
Consensus pattern (87 bp):
AAAAATTCCATTTTTACCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATT
CAATTTTAACCCCAAAACCTCC
Found at i:1402 original size:147 final size:147
Alignment explanation
Indices: 1221--1505 Score: 385
Period size: 147 Copynumber: 1.9 Consensus size: 147
1211 TTTTAACCCT
* * **
1221 AAAAATTTCATTTTTACCCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAAT
1 AAAAATTCCATTTTTACCCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAACTACCAAAAAT
* * *
1286 -TCTAATTTTAACCCTAAAACTTCCAAAAATTCCATTTTACCCTCGAACTACCAAAAATCCCATT
66 CTC-AATTTTAACCCTAAAACTTCCAAAAAGTCCATTTTACCCACAAACTACCAAAAATCCCATT
1350 TTTAACCCCGAAGCTTTC
130 TTTAACCCCGAAGCTTTC
* *
1368 AAAAATTCCATTTTTACCCCCGAACCT-CCAAAAATCCCATTTTTGACCCCAAAACTACCAAAAA
1 AAAAATTCCATTTTTACCCCC-AAACTACCAAAAATCCCATTTTTAACCCCAAAACTACCAAAAA
* * * * ***
1432 TCTCATTTTTAACCCTAAAACTTTCAAAAGGTCCATTTTGCCCACAAACTTTTAAAAATCCCATT
65 TCTCAATTTTAACCCTAAAACTTCCAAAAAGTCCATTTTACCCACAAACTACCAAAAATCCCATT
*
1497 TTTGACCCC
130 TTTAACCCC
1506 AAAATTACCA
Statistics
Matches: 119, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
147 113 0.95
148 6 0.05
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (147 bp):
AAAAATTCCATTTTTACCCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAACTACCAAAAAT
CTCAATTTTAACCCTAAAACTTCCAAAAAGTCCATTTTACCCACAAACTACCAAAAATCCCATTT
TTAACCCCGAAGCTTTC
Found at i:1430 original size:59 final size:59
Alignment explanation
Indices: 1229--1442 Score: 220
Period size: 59 Copynumber: 3.6 Consensus size: 59
1219 CTAAAAATTT
* * * * * * *
1229 CATTTTT-ACCCCCAAACTACCAAAAATCCCATTTTTAACCCCAAAGCTTTCAAAAATTC
1 CATTTTTAACCCCAAAACTACCAAAAATTCCATTTTTACCCCCGAA-CCTCCAAAAATCC
* * * * *
1288 TAATTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTACCCTCGAA-CTACCAAAAATCC
1 CATTTTTAACCCCAAAACTACCAAAAATTCCATTTTTACCCCCGAACCT-CCAAAAATCC
* * **
1346 CATTTTTAACCCCGAAGCTTTCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATCC
1 CATTTTTAACCCCAAAACTACCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATCC
*
1405 CATTTTTGACCCCAAAACTACCAAAAA-TCTCATTTTTA
1 CATTTTTAACCCCAAAACTACCAAAAATTC-CATTTTTA
1443 ACCCTAAAAC
Statistics
Matches: 126, Mismatches: 24, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
57 1 0.01
58 36 0.29
59 67 0.53
60 22 0.17
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (59 bp):
CATTTTTAACCCCAAAACTACCAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATCC
Found at i:1553 original size:28 final size:28
Alignment explanation
Indices: 1504--1562 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1494 ATTTTTGACC
*
1504 CCAAAATTACCATTTCATCCCCGAGAAT
1 CCAAAATTACCATTTCACCCCCGAGAAT
* *
1532 CCAAAATTATCACTTTTACCCCCCGAGAAT
1 CCAAAATTACCA-TTTCA-CCCCCGAGAAT
1562 C
1 C
1563 TGAAAAGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.42
29 4 0.15
30 11 0.42
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (28 bp):
CCAAAATTACCATTTCACCCCCGAGAAT
Found at i:13647 original size:218 final size:218
Alignment explanation
Indices: 13259--13788 Score: 792
Period size: 218 Copynumber: 2.4 Consensus size: 218
13249 ATTATCCACA
* *
13259 AAACAATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACTGAACCAAACCCATGCTCGATG
1 AAACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAACCAAACCCATGCTCGATG
*
13324 TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTGAGAAACATGCCAAAGTAATAAAACA
66 TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTAAGAAACATGCCAAAGTAATAAAACA
* * * * * * *
13389 GTTGGCTTCCTGACCATCTTCTTGATGAGGTACGGAGAAGTGGACCAAATTCGTTTTCCTGATGA
131 GTTAGCTTCCGGACCATCTTCCTGATAAGGTACAGAGAAGTGGACCAAATTCGTCTTCCTAATGA
*
13454 GATACAGAGAAGTGAATTGAAAC
196 GATACAGAGAAGTAAATTGAAAC
*
13477 AAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCGAACCAAACCCATGCTCGATG
1 AAACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAACCAAACCCATGCTCGATG
* * * *
13542 TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTAAGAAGCGTGCCGAAGTAATAAAACG
66 TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTAAGAAACATGCCAAAGTAATAAAACA
*
13607 GTTAGCTTCCGGACCATCTTCCTGATAAGGTACAGAGAAGTGGACCAAATTTGTCTTCCTAATGA
131 GTTAGCTTCCGGACCATCTTCCTGATAAGGTACAGAGAAGTGGACCAAATTCGTCTTCCTAATGA
13672 GATACAGAGAAGTAAATTGAAAC
196 GATACAGAGAAGTAAATTGAAAC
* * * * * * * *
13695 AAATGACGCCGTCATCTTCCCGATGAGACACTGAGAAGAAGACCAAATCAAACTCACGCCTC-AT
1 AAACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAACCAAACCCATG-CTCGAT
* **
13759 GTAAGCAAATCTTCGAACCCCAGCTTCCTG
65 GTGAGCAAATCTTCGAACCATAGCTTCCTG
13789 GTGATACACT
Statistics
Matches: 282, Mismatches: 29, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
218 279 0.99
219 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (218 bp):
AAACGATGCAGTCATCTTCCCGATGAGATACTGAGAAGAAGACCGAACCAAACCCATGCTCGATG
TGAGCAAATCTTCGAACCATAGCTTCCTGATGAGATACTAAGAAACATGCCAAAGTAATAAAACA
GTTAGCTTCCGGACCATCTTCCTGATAAGGTACAGAGAAGTGGACCAAATTCGTCTTCCTAATGA
GATACAGAGAAGTAAATTGAAAC
Done.