Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010044.1 Kokia drynarioides strain JFW-HI SEQ_124812, 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: 4024
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Found at i:331 original size:15 final size:15
Alignment explanation
Indices: 281--339 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
271 GCACTTTATA
*
281 ATTGGACCATTTG-T
1 ATTGGGCCATTTGTT
* * *
295 ATTTGGGTCATCTGTA
1 A-TTGGGCCATTTGTT
*
311 ACTGGGCCATTTGTT
1 ATTGGGCCATTTGTT
326 ATTGGGCCATTTGT
1 ATTGGGCCATTTGT
340 AATTTGGACT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
14 1 0.03
15 32 0.94
16 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (15 bp):
ATTGGGCCATTTGTT
Found at i:405 original size:17 final size:17
Alignment explanation
Indices: 383--428 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
373 TGGACTTTTC
* *
383 TAAATTTAATTTTATAA
1 TAAATTTAAATTTAAAA
400 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
417 TAAACTTAAATT
1 TAAATTTAAATT
429 CAATTTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1164 original size:139 final size:139
Alignment explanation
Indices: 925--2487 Score: 1395
Period size: 139 Copynumber: 11.1 Consensus size: 139
915 ATTCGCTTAT
* ** * * *
925 GAATTTGGTTCACTTCTCAATATCTCATCAGGAAGATTTACTCGCTTCGAGCCTCGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
* * * *
990 TCTTCTCAGTATCTCATCAGGAAGATGATCTCATCGCTGTTTCGACCCGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
1055 CAGGAATAC
131 CAGGAATAC
*
1064 GAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
** ** * *
1129 TCTTCTCAGCATCTCATTGGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
1194 CAGGAATAC
131 CAGGAATAC
*
1203 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
* * * * *
1268 TCTTCTTAGCGTCTCATCGGGAAGATGATCCCATCACTGTTTTGATCCGTTTCTCTATATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
* *
1333 TAGGAAGATTTGCTCGTTTC
131 CAGG-A-A---------TAC
** * *** * * * * * * *
1353 GAGCCTCGTTTGGGTTTTCTTC-TCAGTGTCTCATCAGGAA-A-ATGATC----CCATCGTTATT
1 GAATCT-GGTT--CACTTCTCCGT-A---TCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTT
***** * * * * *** * * * *
1411 TCGACCCGT-TTCTCTGTATCTCATCAGGAATACGAATCTGGTTCACT-TCTCCAT--ATCTCAT
59 T-GGGTTTTCTTCTCAGTGTCTCATCAGGAAGATG-ATC-CCATCACTGTTTCGATCCGTTTC-T
* * * *** **
1472 CAGGAAGATTTGCTCGTTTCG-AGCC
120 C----TG-TAT-CTCATCAGGAATAC
*** * ** * * * * * * * * *
1497 TTGTTTGGGTTTTCTTCTCAGTATCTCATCAGG-A-ATATGATC----CCATCATTGCTTCGATC
1 GAATCT-GGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGT-
** * * * * *** * * ** *
1556 CAT-TTCTCTGTATCTTATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGT-TTTCTTCTCA
64 TTTCTTCTCAGTGTCTCATCAGGAAGA--TGATCCCATC-A--CT-GTTTCGATCCGT-TTCTCT
*
1619 GTGTCTCATCAGGAAGATGATC
122 GTATCTCATCAGG-A-AT-A-C
** * * ** * * *
1641 CCATCGCTGTTTCGGCCCGTTTCTCTATATCTTATCAGGAAGATTTACTCGTTTCGAGCCTCGTT
1 GAAT--CTGGTT---CAC--TTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTT
* * * *
1706 TGAGTTTTCTTCTCAGTGTCTCATCAGGAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTGT
59 TGGGTTTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGT
1771 ATCTCATCAGGAATAC
124 ATCTCATCAGGAATAC
*
1787 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
* *
1852 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCATTGTTTCGATCTGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
1917 CAGGAATAC
131 CAGGAATAC
* *
1926 GAATCTTGCTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTT-TTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
* * *
1990 TCTTCTCAGTGTCTCATCAGAAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
2055 CAGGAATAC
131 CAGGAATAC
*
2064 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
* * * *
2129 TCTTCTCGGTGTCTCATCAGGAAGATGATCACATCATTGTTTCGATCCGTTTCTCTATATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
2194 CAGGAATAC
131 CAGGAATAC
*
2203 GAATCTGGCTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
*
2268 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCATTGTTTCGATCCGTTTCTCTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
2333 CAGGAATAC
131 CAGGAATAC
* *
2342 GAATCTGGCTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTATTTGGGTTT
1 GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
* * * * *
2407 TCTTTTCAGTGTTTCACCAGGACGATGATCCCATCACTGTTTCGATCCGTTTCTTTGTATCTCAT
66 TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
*
2472 CAGGAAGAC
131 CAGGAATAC
2481 GAATCTG
1 GAATCTG
2488 CTTTGTGGAT
Statistics
Matches: 1181, Mismatches: 182, Indels: 122
0.80 0.12 0.08
Matches are distributed among these distances:
138 132 0.11
139 827 0.70
140 6 0.01
141 6 0.01
142 9 0.01
143 1 0.00
144 16 0.01
145 6 0.01
146 6 0.01
147 1 0.00
148 3 0.00
149 4 0.00
150 72 0.06
151 15 0.01
152 11 0.01
153 7 0.01
154 10 0.01
155 4 0.00
156 45 0.04
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (139 bp):
GAATCTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTT
TCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGTTTCTCTGTATCTCAT
CAGGAATAC
Found at i:1378 original size:241 final size:241
Alignment explanation
Indices: 1077--2060 Score: 1142
Period size: 241 Copynumber: 4.1 Consensus size: 241
1067 TTTGGTTCAC
* * **
1077 TTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGCATC
1 TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
**
1142 TCATTGGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAAT
66 TCATCAGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAAT
1207 CTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTT
131 CTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTT
* * * *
1272 CTTAGCGTCTCATCGGGAAGATGATCCCATCACTGTTTTGATCCGT
196 CTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGT
* *
1318 TTCTCTATATCTCATTAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
1 TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
* * *
1383 TCATCAGGAAAATGATCCCATCGTTATTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAAT
66 TCATCAGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAAT
* *
1448 CTGGTTCACTTCTCCATATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTTTCTT
131 CTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTT
* * * * *
1513 CTCAGTATCTCATCAGGAATATGATCCCATCATTGCTTCGATCCAT
196 CTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGT
*
1559 TTCTCTGTATCTTATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
1 TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
* * *
1624 TCATCAGGAAGATGATCCCATCGCTGTTTCGGCCCGTTTCTCTATATCTTATCAGGAAGATTTAC
66 TCATCAGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGG-A-A--TA-
* ** * * * * ***
1689 TCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAGG-A-ATATGATCCCATC--G-
126 ------CGA--ATC---TG-GTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGC
* **** * * ** *
1749 C-TGTTTCGACCCGT-TTCTCTGTATCTCATCAGG-A-AT-A-CGAAT--CTGGTTC-A--C-T
179 CTTGTTTAG-GTTTTCTTCTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGT
* * *
1801 -TCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTGTC
1 TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
** * *
1865 TCATCAGGAAGATGATCCCATCATTGTTTCGATCTGTTTCTCTGTATCTCATCAGGAATACGAAT
66 TCATCAGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAAT
* * *
1930 CTTGCTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTT-TTTGGGTTTTCTT
131 CTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTT
* * *
1994 CTCAGTGTCTCATCAGAAAGATGATCCCATCGCTGTTTCGACCCGT
196 CTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGT
2040 TTCTCTGTATCTCATCAGGAA
1 TTCTCTGTATCTCATCAGGAA
2061 TACGAATCTG
Statistics
Matches: 620, Mismatches: 87, Indels: 73
0.79 0.11 0.09
Matches are distributed among these distances:
224 20 0.03
225 2 0.00
226 8 0.01
228 4 0.01
229 21 0.03
230 5 0.01
231 2 0.00
232 1 0.00
233 3 0.00
235 6 0.01
236 1 0.00
237 2 0.00
238 1 0.00
239 2 0.00
240 20 0.03
241 440 0.71
242 2 0.00
243 2 0.00
245 3 0.00
246 5 0.01
248 3 0.00
249 1 0.00
250 2 0.00
251 1 0.00
252 27 0.04
253 2 0.00
254 3 0.00
256 8 0.01
257 3 0.00
258 20 0.03
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.38
Consensus pattern (241 bp):
TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
TCATCAGGAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAAT
CTGGTTCACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTT
CTCAGTGTCTCATCAGGAAGATGATCCCATCACTGTTTCGATCCGT
Found at i:1398 original size:102 final size:102
Alignment explanation
Indices: 1223--1440 Score: 319
Period size: 102 Copynumber: 2.1 Consensus size: 102
1213 CACTTCTCCG
* * *
1223 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTTCTTAGCGTCTCATCGG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTTTTCTTCTCAGCGTCTCATCAG
* * * *
1288 GAAGATGATCCCATCACTGTTTTGATCCGTTTCTCTA
66 GAAAATGATCCCATCACTATTTCGACCCGTTTCTCTA
* * *
1325 TATCTCATTAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTTTTCTTCTCAGCGTCTCATCAG
** *
1390 GAAAATGATCCCATCGTTATTTCGACCCGTTTCTCTG
66 GAAAATGATCCCATCACTATTTCGACCCGTTTCTCTA
1427 TATCTCATCAGGAA
1 TATCTCATCAGGAA
1441 TACGAATCTG
Statistics
Matches: 102, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (102 bp):
TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTTTTCTTCTCAGCGTCTCATCAG
GAAAATGATCCCATCACTATTTCGACCCGTTTCTCTA
Found at i:1633 original size:102 final size:102
Alignment explanation
Indices: 1464--1783 Score: 514
Period size: 102 Copynumber: 3.1 Consensus size: 102
1454 CACTTCTCCA
* *
1464 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTATCTCATCAG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
** * * *
1529 GAATATGATCCCATCATTGCTTCGATCCATTTCTCTG
66 GAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTG
*
1566 TATCTTATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
* * *
1631 GAAGATGATCCCATCGCTGTTTCGGCCCGTTTCTCTA
66 GAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTG
* * *
1668 TATCTTATCAGGAAGATTTACTCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
1733 GAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTG
66 GAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTG
1770 TATCTCATCAGGAA
1 TATCTCATCAGGAA
1784 TACGAATCTG
Statistics
Matches: 201, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 201 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (102 bp):
TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
GAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTG
Found at i:1715 original size:343 final size:343
Alignment explanation
Indices: 1216--1922 Score: 1189
Period size: 343 Copynumber: 2.1 Consensus size: 343
1206 TCTGGTTCAC
* * *
1216 TTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTAGGTTTTCTTCTTAGCGTC
1 TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTTTTCTTCTCAGCGTC
* * * * *
1281 TCATCGGGAAGATGATCCCATCACTGTTTTGATCCGTTTCTCTATATCTCATTAGGAAGATTTGC
66 TCATCAGGAAGATGATCCCATCACTGTTTCGACCCGTTTCTCTATATCTCATCAGGAAGATTTAC
* *
1346 TCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTCTCATCAGGAAAATGATCCCATCGTTATT
131 TCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAGGAAAATGATCCCATCGCTATT
1411 TCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCACTTCTCCATATCTCATCAGG
196 TCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCACTTCTCCATATCTCATCAGG
* *
1476 AAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTATCTCATCAGGAATATGATCCC
261 AAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTATCTCATCAGGAAGATGATCCC
1541 ATCATTGCTTCGATCCAT
326 ATCATTGCTTCGATCCAT
* * *
1559 TTCTCTGTATCTTATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTGGGTTTTCTTCTCAGTGTC
1 TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTTTTCTTCTCAGCGTC
* * *
1624 TCATCAGGAAGATGATCCCATCGCTGTTTCGGCCCGTTTCTCTATATCTTATCAGGAAGATTTAC
66 TCATCAGGAAGATGATCCCATCACTGTTTCGACCCGTTTCTCTATATCTCATCAGGAAGATTTAC
* *
1689 TCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAGGAATATGATCCCATCGCTGTT
131 TCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAGGAAAATGATCCCATCGCTATT
*
1754 TCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCACTTCTCCGTATCTCATCAGG
196 TCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCACTTCTCCATATCTCATCAGG
*
1819 AAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTGTCTCATCAGGAAGATGATCCC
261 AAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTATCTCATCAGGAAGATGATCCC
* **
1884 ATCATTGTTTCGATCTGT
326 ATCATTGCTTCGATCCAT
1902 TTCTCTGTATCTCATCAGGAA
1 TTCTCTGTATCTCATCAGGAA
1923 TACGAATCTT
Statistics
Matches: 338, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
343 338 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.39
Consensus pattern (343 bp):
TTCTCTGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTCGTTTAGGTTTTCTTCTCAGCGTC
TCATCAGGAAGATGATCCCATCACTGTTTCGACCCGTTTCTCTATATCTCATCAGGAAGATTTAC
TCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAGGAAAATGATCCCATCGCTATT
TCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCACTTCTCCATATCTCATCAGG
AAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTATCTCATCAGGAAGATGATCCC
ATCATTGCTTCGATCCAT
Found at i:2203 original size:277 final size:277
Alignment explanation
Indices: 1668--2487 Score: 1406
Period size: 277 Copynumber: 3.0 Consensus size: 277
1658 CGTTTCTCTA
* * * *
1668 TATCTTATCAGGAAGATTTACTCGTTTCGAGCCTCGTTTGAGTTTTCTTCTCAGTGTCTCATCAG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCT-TTTTGGGTTTTCTTCTCAGTGTCTCATCAG
*
1733 GAATATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTC
65 GAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTC
1798 ACTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTG
130 ACTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTG
*
1863 TCTCATCAGGAAGATGATCCCATCATTGTTTCGATCTGTTTCTCTGTATCTCATCAGGAATACGA
195 TCTCATCAGGAAGATGATCCCATCATTGTTTCGATCCGTTTCTCTGTATCTCATCAGGAATACGA
*
1928 ATCTTGCTCACTTCTCCG
260 ATCTGGCTCACTTCTCCG
*
1946 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTTTTGGGTTTTCTTCTCAGTGTCTCATCAGA
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTTTTGGGTTTTCTTCTCAGTGTCTCATCAGG
2011 AAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCA
66 AAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCA
*
2076 CTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCGGTGT
131 CTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTGT
* *
2141 CTCATCAGGAAGATGATCACATCATTGTTTCGATCCGTTTCTCTATATCTCATCAGGAATACGAA
196 CTCATCAGGAAGATGATCCCATCATTGTTTCGATCCGTTTCTCTGTATCTCATCAGGAATACGAA
2206 TCTGGCTCACTTCTCCG
261 TCTGGCTCACTTCTCCG
2223 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTGTCTCATCAG
1 TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTT-TTTGGGTTTTCTTCTCAGTGTCTCATCAG
** * *
2288 GAAGATGATCCCATCATTGTTTCGATCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGCTC
65 GAAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTC
* * *
2353 ACTTCTCCGTATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTATTTGGGTTTTCTTTTCAGTG
130 ACTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTG
* * * * * *
2418 TTTCACCAGGACGATGATCCCATCACTGTTTCGATCCGTTTCTTTGTATCTCATCAGGAAGACGA
195 TCTCATCAGGAAGATGATCCCATCATTGTTTCGATCCGTTTCTCTGTATCTCATCAGGAATACGA
2483 ATCTG
260 ATCTG
2488 CTTTGTGGAT
Statistics
Matches: 513, Mismatches: 28, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
277 269 0.52
278 244 0.48
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (277 bp):
TATCTCATCAGGAAGATTTGCTCGTTTCGAGCCTTTTTGGGTTTTCTTCTCAGTGTCTCATCAGG
AAGATGATCCCATCGCTGTTTCGACCCGTTTCTCTGTATCTCATCAGGAATACGAATCTGGTTCA
CTTCTCCGTATCTCATCAGGAAGATTTACTCGTTTCGAGCCTTGTTTGGGTTTTCTTCTCAGTGT
CTCATCAGGAAGATGATCCCATCATTGTTTCGATCCGTTTCTCTGTATCTCATCAGGAATACGAA
TCTGGCTCACTTCTCCG
Done.