Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012642.1 Kokia drynarioides strain JFW-HI SEQ_127652, 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: 10010
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:353 original size:17 final size:16
Alignment explanation
Indices: 331--403 Score: 92
Period size: 17 Copynumber: 4.4 Consensus size: 16
321 TTGGACTTTT
**
331 TAAATTTATTTTTATAA
1 TAAATTTAAATTTA-AA
348 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
365 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
382 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
398 TAAATT
1 TAAATT
404 CAATTTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.16
17 41 0.82
18 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:382 original size:7 final size:6
Alignment explanation
Indices: 348--398 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
338 ATTTTTATAA
* *
348 TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT TAAATT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
394 TAAAT
1 TAAAT
399 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 5 0.13
6 27 0.71
7 3 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:415 original size:16 final size:17
Alignment explanation
Indices: 346--416 Score: 92
Period size: 17 Copynumber: 4.3 Consensus size: 17
336 TTATTTTTAT
346 AATAAATTTAAATTTCA
1 AATAAATTTAAATTTCA
*
363 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTCA
*
380 AATAAACTTAAATTT-A
1 AATAAATTTAAATTTCA
* *
396 AATAAA-TTCAATTTCC
1 AATAAATTTAAATTTCA
412 AATAA
1 AATAA
417 GTCCAGACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
15 7 0.14
16 12 0.24
17 30 0.61
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (17 bp):
AATAAATTTAAATTTCA
Found at i:1494 original size:201 final size:202
Alignment explanation
Indices: 737--1591 Score: 1300
Period size: 200 Copynumber: 4.3 Consensus size: 202
727 GTATCTCATT
** * *
737 GGGAGAGTGACTGCGTCGCCTGTTTCAA-TCCGCTTCTTTGTATCTCATCAAGAAGACGAATTTG
1 GGGAGA-TGACTGCGTCGTTTGTTTCAACT-CGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
* *
801 GTTCATTTCAC-AGTATCTCATCAGGAAGCTAACCATTTA--GCTTCCACCTGCTTCTCAGTGTC
64 GTTCACTTCTCTAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
** * *
863 TCATTAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGT
129 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGT
928 GTCTCATCA
194 GTCTCATCA
* * * * * * * **
937 GGAAGATG-GTCCCATC-ATCGTTTTAA-TCCGCTTCTCCATATCTCATCAGGAAGACGAATTTG
1 GGGAGATGACT-GCGTCGTTTGTTTCAACT-CGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
* *
999 GTTCACTTC-CCAGTATTTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
64 GTTCACTTCTCTAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
1063 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGT
129 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGT
1128 GTCTCATCA
194 GTCTCATCA
* * * *
1137 GGGAGATGATTGCGTCTTTTGTTTCAACTCGCTTCTCTGTATCTCATCAAG-ATACGAATTTGGT
1 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGT
* *
1201 TCACTTCTCT-GTATCTCACCAGGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTCTC
66 TCACTTCTCTAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTC
*
1265 ATCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGT
131 ATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGT
1330 CTCATCA
196 CTCATCA
*
1337 GGGAGATGACTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATTTGGT
1 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGT
1402 TCACTTCTCTA-TATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTC
66 TCACTTCTCTAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTC
* * *
1466 ATTGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCGTTAGTGT
131 ATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGT
1531 CTCATCA
196 CTCATCA
*
1538 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATTAGGAAG
1 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAG
1592 CTAACCATTT
Statistics
Matches: 598, Mismatches: 47, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
197 1 0.00
198 74 0.12
199 5 0.01
200 296 0.49
201 221 0.37
202 1 0.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (202 bp):
GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGT
TCACTTCTCTAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTC
ATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGT
CTCATCA
Found at i:1582 original size:401 final size:399
Alignment explanation
Indices: 737--1584 Score: 1310
Period size: 401 Copynumber: 2.1 Consensus size: 399
727 GTATCTCATT
** *
737 GGGAGAGTGACTGCGTCGCCTGTTTCAA-TCCGCTTCTTTGTATCTCATCAAGAAGACGAATTTG
1 GGGAGA-TGACTGCGTCGTTTGTTTCAACT-CGCTTCTCTGTATCTCATCAAGAAGACGAATTTG
* *
801 GTTCATTTCACAGTATCTCATCAGGAAGCTAACCATTTAGCTTCCACCTGCTTCTCAGTGTCTCA
64 GTTCACTTCACAGTATCTCACCAGGAAGCTAACCATTTAGCTTCCACCTGCTTCTCAGTGTCTCA
* *
866 TTAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTC
129 TCAGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTC
* * *
931 TCATCAGGAAGATGGTCCCATCATCGTTTTAATCCGCTTCTCCATATCTCATCAGGAAGACGAAT
194 TCATCAGGAAGATGCTCCCATCATCGTTTCAATCCACTTCTCCATATCTCATCAGGAAGACGAAT
*
996 TTGGTTCACTTCCCAGTATTTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTG
259 TTGGTTCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTG
1061 TCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCA
324 TCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCA
1126 GTGTCTCATCA
389 GTGTCTCATCA
* * *
1137 GGGAGATGATTGCGTCTTTTGTTTCAACTCGCTTCTCTGTATCTCATCAAG-ATACGAATTTGGT
1 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGT
* * *
1201 TCACTTCTCTGTATCTCACCAGGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTCTCA
66 TCACTTCACAGTATCTCACCAGGAAGCTAACCATTTA--GCTTCCACCTGCTTCTCAGTGTCTCA
* * *
1266 TCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTC
129 TCAGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTC
* * * * * **
1331 TCATCAGGGAGATGACT-GCGTCGTTTGTTTCAA-CTCACTTCTCTGTATCTCATCAGGAAGACG
194 TCATCAGGAAGATG-CTCCCATC-ATCGTTTCAATC-CACTTCTCCATATCTCATCAGGAAGACG
*
1394 AATTTGGTTCACTTCTCTA-TATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTC
256 AATTTGGTTCACTTC-CCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTC
*
1458 AGTGTCTCATTGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTC
320 AGTGTCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTC
* *
1523 GTTAGTGTCTCATCA
385 CTCAGTGTCTCATCA
1538 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCAT
1 GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCAT
1585 TAGGAAGCTA
Statistics
Matches: 408, Mismatches: 33, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
398 44 0.11
399 38 0.09
400 110 0.27
401 214 0.52
402 2 0.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (399 bp):
GGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGGT
TCACTTCACAGTATCTCACCAGGAAGCTAACCATTTAGCTTCCACCTGCTTCTCAGTGTCTCATC
AGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTCTC
ATCAGGAAGATGCTCCCATCATCGTTTCAATCCACTTCTCCATATCTCATCAGGAAGACGAATTT
GGTTCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGT
GTCTCATCA
Found at i:1676 original size:164 final size:164
Alignment explanation
Indices: 1405--1755 Score: 648
Period size: 164 Copynumber: 2.1 Consensus size: 164
1395 ATTTGGTTCA
* *
1405 CTTCTCTATATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATTG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
* * *
1470 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCGTTAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
1535 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
*
1569 CTTCTCTGTATCTCATTAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1634 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
1699 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
1733 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
1756 ACGAATTTGG
Statistics
Matches: 180, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
164 180 1.00
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (164 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
Found at i:1810 original size:201 final size:201
Alignment explanation
Indices: 1569--2727 Score: 2005
Period size: 201 Copynumber: 5.8 Consensus size: 201
1559 TTTCAACTCG
*
1569 CTTCTCTGTATCTCATTAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
*
1634 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCA
1699 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
1764 GGTTCA
196 GGTTCA
* * *
1770 CTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTCTTATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1835 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTC-GATGTCTC
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAG-TGTCTC
1899 ATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATT
130 ATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATT
1964 TGGTTCA
195 TGGTTCA
* * *
1971 CTTCTCTATATCTCATCAGGAAGCTAACCATTTATTGCTTTCCACCTGCTTCTCAATGTCTTATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGC-TTCCACCTGCTTCTCAGTGTCTCATC
* * *
2036 GAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTAAGCCTCGTTTGGGTCTTCTCCTTAGTGTCTC
65 GGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTC
* *
2101 ATCAGGGAGATGATTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATT
130 ATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATT
2166 TGGTTCA
195 TGGTTCA
*
2173 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTTAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
*
2238 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCA
* * *
2303 TCAAGGAGATGACTGCGTCATTTGTTTCAACTCGCTTCTTTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
*
2368 GCTTCA
196 GGTTCA
*
2374 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTACTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
* *
2439 GGAAGCTGGGGTTCAAAGATTTTGTTCACTTTGAGCCTCGTTTGGGTTTTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCA
*
2504 TCAGGGAGATGACTGGGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
2569 GGTTCA
196 GGTTCA
* * * *
2575 CTTCTCTGTATCTCATCAAGAAGGTAACCTTTTATTGCTTCCACCTGCTTCTCAATGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
* * *
2640 GGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCTTCGTTTAGGTCTTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCA
* *
2705 TCAGGGAGATGACTACGTTGTTT
131 TCAGGGAGATGACTGCGTCGTTT
2728 TGTGGATAAT
Statistics
Matches: 904, Mismatches: 51, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
200 1 0.00
201 710 0.79
202 192 0.21
203 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCA
TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
GGTTCA
Found at i:1874 original size:365 final size:365
Alignment explanation
Indices: 1204--1956 Score: 1373
Period size: 365 Copynumber: 2.1 Consensus size: 365
1194 ATTTGGTTCA
* *
1204 CTTCTCTGTATCTCACCAGGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
*
1269 GGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGTGTCTCA
66 GGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
1334 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATTT
*
1399 GGTTCACTTCTCTATATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
196 GGTTCACTTCTCTATATCTCATCAAGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
* *
1464 TCATTGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCGTTAG-
261 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTC-CTAGA
1528 TGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
325 TGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
*
1569 CTTCTCTGTATCTCATTAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
*
1634 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
66 GGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
*
1699 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATTT
* *
1764 GGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTC
196 GGTTCACTTCTCTATATCTCATCAAGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
* *
1829 TTATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCGAT
261 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTAGAT
1894 GTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
326 GTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
1934 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
1957 ACGAATTTGG
Statistics
Matches: 373, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
364 2 0.01
365 371 0.99
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (365 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
GGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATTT
GGTTCACTTCTCTATATCTCATCAAGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTC
TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTAGAT
GTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCG
Found at i:2111 original size:403 final size:402
Alignment explanation
Indices: 1569--2727 Score: 2023
Period size: 403 Copynumber: 2.9 Consensus size: 402
1559 TTTCAACTCG
*
1569 CTTCTCTGTATCTCATTAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
1634 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
1699 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
1764 GGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTC
196 GGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTC
*
1829 TTATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTC-GA
261 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAG-
1893 TGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGA
325 TGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGA
*
1958 CGAATTTGGTTCA
390 CGAATTTGCTTCA
* * *
1971 CTTCTCTATATCTCATCAGGAAGCTAACCATTTATTGCTTTCCACCTGCTTCTCAATGTCTTATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGC-TTCCACCTGCTTCTCAGTGTCTCATC
* * * *
2036 GAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTAAGCCTCGTTTGGGTCTTCTCCTTAGTGTCTC
65 GGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTC
* *
2101 ATCAGGGAGATGATTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAGGAAGACGAATT
130 ATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATT
* * *
2166 TGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTTAGTGT
195 TGGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGT
*
2231 CTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTCCTCAG
260 CTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAG
* * *
2296 TGTCTCATCAAGGAGATGACTGCGTCATTTGTTTCAACTCGCTTCTTTGTATCTCATCAGGAAGA
325 TGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGA
2361 CGAATTTGCTTCA
390 CGAATTTGCTTCA
*
2374 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTACTTCCACCTGCTTCTCAGTGTCTCATCG
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
* *
2439 GGAAGCTGGGGTTCAAAGATTTTGTTCACTTTGAGCCTCGTTTGGGTTTTCTCCTCAGTGTCTCA
66 GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
*
2504 TCAGGGAGATGACTGGGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
131 TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
* *
2569 GGTTCACTTCTCTGTATCTCATCAAGAAGGTAACCTTTTATTGCTTCCACCTGCTTCTCAATGTC
196 GGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTC
* * *
2634 TCATCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCTTCGTTTAGGTCTTCTCCTCAGT
261 TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGT
* *
2699 GTCTCATCAGGGAGATGACTACGTTGTTT
326 GTCTCATCAGGGAGATGACTGCGTCGTTT
2728 TGTGGATAAT
Statistics
Matches: 711, Mismatches: 44, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
402 329 0.46
403 381 0.54
404 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (402 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCG
GGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCA
TCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGACGAATTT
GGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTC
TCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAGT
GTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATCAGGAAGAC
GAATTTGCTTCA
Found at i:2302 original size:969 final size:965
Alignment explanation
Indices: 737--2560 Score: 3039
Period size: 969 Copynumber: 1.9 Consensus size: 965
727 GTATCTCATT
*
737 GGGAGAGTGACTGCGTCGCCTGTTTCAATCCGCTTCTTTGTATCTCATCAAGAAGACGAATTTGG
1 GGGAGAGTGACTGCGTCGCCTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGG
* *
802 TTCATTTCACAGTATCTCATCAGGAAGCTAACCATTTAGCTTCCACCTGCTTCTCAGTGTCTCAT
66 TTCACTTCACAGTATCTCATCAAGAAGCTAACCATTTAGCTTCCACCTGCTTCTCAGTGTCTCAT
*
867 TAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTCT
131 CAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTCT
* *
932 CATCAGGAAGATGGTCCCATCATCGTTTTAATCCGCTTCTCCATATCTCATCAGGAAGACGAATT
196 CATCAGGAAGATGCTCCCATCATCGTTTCAATCCGCTTCTCCATATCTCATCAGGAAGACGAATT
* *
997 TGGTTCACTTCCCAGTATTTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGT
261 TGGTTCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAATGT
* *
1062 CTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTCAG
326 CTCATCGAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTAAGCCTCGTTTGGGTCTTCTCCTCAG
* * *
1127 TGTCTCATCAGGGAGATGATTGCGTCTTTTGTTTCAACTCGCTTCTCTGTATCTCATCAAGATAC
391 TGTCTCATCAGGGAGATGATTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAAGAGAC
*
1192 GAATTTGGTTCACTTCTCTGTATCTCACCAGGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTC
456 GAATTTGGTTCACTTCTCTGTATCTCACCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTC
*
1257 AGTGTCTCATCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTC
521 AGTGTCTCATCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTC
* *
1322 CTCAGTGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAG
586 CTCAGTGTCTCATCAAGGAGATGACTGCGTCATTTGTTTCAACTCACTTCTCTGTATCTCATCAG
* *
1387 GAAGACGAATTTGGTTCACTTCTCTATATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTG
651 GAAGACGAATTTGCTTCACTTCTCTATATCTCATCAGGAAGCTAACCATTTATTACTTCCACCTG
*
1452 CTTCTCAGTGTCTCATTGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGT
716 CTTCTCAGTGTCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGT
* *
1517 CTTCTCGTTAGTGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCT
781 CTTCTCCTCAGTGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCT
*
1582 CATTAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCGGGAAGCTGGGGTT
846 CATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCGGGAAGCTGGGGTT
1647 CAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCA
911 CAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCA
** *
1702 GGGAGA-TGACTGCGTCGTTTGTTTCAA-CTCGCTTCTCTGTATCTCATCAGGAAGACGAATTTG
1 GGGAGAGTGACTGCGTCGCCTGTTTCAATC-CGCTTCTCTGTATCTCATCAAGAAGACGAATTTG
* * *
1765 GTTCACTTCTCTGTATCTCATCAAGAAGCTAACCTTTTATTGCTTCCACCTGCTTCTCAGTGTCT
65 GTTCACTTCACAGTATCTCATCAAGAAGCTAACCATTTA--GCTTCCACCTGCTTCTCAGTGTCT
* * * *
1830 TATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTCCTC-GAT
128 CATCAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAG-T
* * * * * **
1894 GTCTCATCAGGGAGATGACT-GCGTCGTTTGTTTCAA-CTCGCTTCTCTGTATCTCATCAGGAAG
192 GTCTCATCAGGAAGATG-CTCCCATC-ATCGTTTCAATC-CGCTTCTCCATATCTCATCAGGAAG
*
1957 ACGAATTTGGTTCACTTCTCTA-TATCTCATCAGGAAGCTAACCATTTATTGCTTTCCACCTGCT
254 ACGAATTTGGTTCACTTC-CCAGTATCTCATCAGGAAGCTAACCATTTATTGC-TTCCACCTGCT
*
2021 TCTCAATGTCTTATCGAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTAAGCCTCGTTTGGGTCT
317 TCTCAATGTCTCATCGAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTAAGCCTCGTTTGGGTCT
*
2086 TCTCCTTAGTGTCTCATCAGGGAGATGATTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCA
382 TCTCCTCAGTGTCTCATCAGGGAGATGATTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCA
* *
2151 TCAGGAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCA
447 TCAAG-AGACGAATTTGGTTCACTTCTCTGTATCTCACCAGGAAGCTAACCATTTATTGCTTCCA
* *
2216 CCTGCTTCTTAGTGTCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCATTT
511 CCTGCTTCTCAGTGTCTCATCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCATTT
* *
2281 GGGTCTTCTCCTCAGTGTCTCATCAAGGAGATGACTGCGTCATTTGTTTCAACTCGCTTCTTTGT
576 GGGTCTTCTCCTCAGTGTCTCATCAAGGAGATGACTGCGTCATTTGTTTCAACTCACTTCTCTGT
*
2346 ATCTCATCAGGAAGACGAATTTGCTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTATTA
641 ATCTCATCAGGAAGACGAATTTGCTTCACTTCTCTATATCTCATCAGGAAGCTAACCATTTATTA
*
2411 CTTCCACCTGCTTCTCAGTGTCTCATCGGGAAGCTGGGGTTCAAAGATTTTGTTCACTTTGAGCC
706 CTTCCACCTGCTTCTCAGTGTCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCC
* *
2476 TCGTTTGGGTTTTCTCCTCAGTGTCTCATCAGGGAGATGACTGGGTCGTTTGTTTCAACTCGCTT
771 TCGTTTGGGTCTTCTCCTCAGTGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTT
2541 CTCTGTATCTCATCAGGAAG
836 CTCTGTATCTCATCAGGAAG
2561 ACGAATTTGG
Statistics
Matches: 796, Mismatches: 53, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
963 1 0.00
964 85 0.11
965 7 0.01
966 101 0.13
967 78 0.10
968 140 0.18
969 384 0.48
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.36
Consensus pattern (965 bp):
GGGAGAGTGACTGCGTCGCCTGTTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACGAATTTGG
TTCACTTCACAGTATCTCATCAAGAAGCTAACCATTTAGCTTCCACCTGCTTCTCAGTGTCTCAT
CAGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTCAGCCTCATTTGGGTCTTCTCCTCAGTGTCT
CATCAGGAAGATGCTCCCATCATCGTTTCAATCCGCTTCTCCATATCTCATCAGGAAGACGAATT
TGGTTCACTTCCCAGTATCTCATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAATGT
CTCATCGAGAAGCTGGGGTTCAAAGATTTTGCTCACTTTAAGCCTCGTTTGGGTCTTCTCCTCAG
TGTCTCATCAGGGAGATGATTGCGTCGTTTGTTTCAACTCACTTCTCTGTATCTCATCAAGAGAC
GAATTTGGTTCACTTCTCTGTATCTCACCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTC
AGTGTCTCATCGGGAAGCTGAGGTTCAAAGATTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTC
CTCAGTGTCTCATCAAGGAGATGACTGCGTCATTTGTTTCAACTCACTTCTCTGTATCTCATCAG
GAAGACGAATTTGCTTCACTTCTCTATATCTCATCAGGAAGCTAACCATTTATTACTTCCACCTG
CTTCTCAGTGTCTCATCGGGAAGCTGGGGTTCAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGT
CTTCTCCTCAGTGTCTCATCAGGGAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCT
CATCAGGAAGCTAACCATTTATTGCTTCCACCTGCTTCTCAGTGTCTCATCGGGAAGCTGGGGTT
CAAAGATTTTGCTCACTTTGAGCCTCGTTTGGGTATTCTCCTCAGTGTCTCATCA
Found at i:3195 original size:27 final size:27
Alignment explanation
Indices: 3165--3225 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
3155 CCAAGAATTT
*
3165 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
** *
3192 TATTAAAGGGAGGGTCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
3219 TCATTAA
1 T-ATTAA
3226 TTGAAAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.51, C:0.08, G:0.23, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Done.