Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008123.1 Kokia drynarioides strain JFW-HI SEQ_122781, 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: 8174
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Found at i:1137 original size:20 final size:22
Alignment explanation
Indices: 1093--1145 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
1083 ATATTTTTTG
*
1093 TTTTTCT-TTTCTTCTTTGTCC
1 TTTTTCTCTTTGTTCTTTGTCC
1114 -TTTTCTCTTTGTT-TTT-TCC
1 TTTTTCTCTTTGTTCTTTGTCC
*
1133 TTTTTGTCTTTGT
1 TTTTTCTCTTTGT
1146 GCTTCTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 3 0.11
20 20 0.71
21 5 0.18
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.74
Consensus pattern (22 bp):
TTTTTCTCTTTGTTCTTTGTCC
Found at i:1974 original size:41 final size:42
Alignment explanation
Indices: 1917--2052 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 42
1907 TCTTGGTTTA
* ** * *
1917 GGGGTAAAAGATTGGATGGTGGCTTTAACCTGTCCCA-TATC
1 GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
* * *
1958 GGGGTAAGAGATTGGATGACATCTTCAATCTGCCCCATTATC
1 GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
* *
2000 -GGGTAAGAGATTGGAT-G--GCTTCAACCTGCCCCGTGATC
1 GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
* *
2038 AGGGTAAAAGATTGG
1 GGGGTAAGAGATTGG
2053 TGTGTTTTCA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 17 0.22
39 13 0.16
41 45 0.57
42 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (42 bp):
GGGGTAAGAGATTGGATGGCAGCTTCAACCTGCCCCATTATC
Found at i:2670 original size:39 final size:37
Alignment explanation
Indices: 1950--3618 Score: 362
Period size: 38 Copynumber: 42.6 Consensus size: 37
1940 TTTAACCTGT
*
1950 CCCAT-ATCGGGGTAAGAGATTGGATGACATCTTCAATCTG
1 CCCATGATCGGGGTAAGAGATTGGA-G--GT-TTCAATCTG
* * *
1990 CCCCATTATC-GGGTAAGAGATTGGATGGCTTCAACCTG
1 -CCCATGATCGGGGTAAGAGATTGGA-GGTTTCAATCTG
* * * * *
2028 CCCCGTGATCAGGGTAAAAGATTGGTGTGTTTTCAATCTAA
1 -CCCATGATCGGGGTAAGAGATTGGAG-G-TTTCAATCT-G
* ** * **
2069 CCCTCTGATTAGGGTAAAAGATT-GAATTCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGT-TTCAATCTG
* * * *
2107 CCCCATAATCGGGGTAAGAGATTGGTGTCTCTTCAAT-TT
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* *** * * * *
2146 CCCTCTGATTATGATAAAAGATCGGATGTTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
** * *
2184 CCTCATGATCAAGGTAAGAGATTGGTGTGTCTTCAATCTA
1 CC-CATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * ** *
2224 CCCTCTGATTAGGGTAAAATATCAGATGG-TTCAATATG
1 CCC-ATGATCGGGGTAAGAGATTGGA-GGTTTCAATCTG
* * ** *
2262 TCCCATGATCAGGGCAAGAGATTAATATGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATT-GGAGGT-TTCAATCTG
** * * * * * *
2302 CGCTC-TGATTAGGGTAAAAGATCGAATGCTTCTATCTG
1 C-C-CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * * *
2340 TACCATGATCGGGATAAGAGATTGGTGTATCTTCAATCTA
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * * *
2380 CCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * *
2418 CCTCATGATTGGGGTAAGAGATTAGTGTGTCTTCAATCTA
1 CC-CATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * * * * *
2458 CCCTCTGATTAGGGTAAAAGATCGAATGCTTCTATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * *
2496 CCCCATGATTGGGGTAAGAGATTGGTGTGTCTTTAATTTG
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* * ** **
2536 CCCTCTAATTAGGGTAAGAGATTGGATATTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
2574 CCCCATGATCGGGGTAAGAGATTGGATGATGTTTACAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGA-G--GTTT-CAATCTG
* * **
2616 CCCTCTAATTAGGGTAAGAGATTGGACGGTTGT-AATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGA-GGTT-TCAATCTG
* *
2655 TCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTA
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * ** * *
2695 CCCTCTGATTAGGGTAAAAGATCAGATGCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
2733 TCCCATGATCGGGGTAAGAGATTGGAGTGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* * ** * * * *
2773 CCCTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * * *
2811 CCTCATGATTGGGGTAAAAGATTGAATGTCTTCAATCTG
1 CC-CATGATCGGGGTAAGAGATTGGAGGT-TTCAATCTG
* * ** * **
2850 CCCTCTAATTAGGGTAAAAGATTGGTTGTTTCAATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * *
2888 CCTCGTGATCGGGGTAAGAGATTGGATGATGTTTTCAATTTA
1 CC-CATGATCGGGGTAAGAGATTGGA-G--G-TTTCAATCTG
* * * *** * * *
2930 CCCTCTAATTGGGGTAAGAGATTGGACAACTACTATCTAT
1 CCC-ATGATCGGGGTAAGAGATTGGA-GGTTTCAATCT-G
* *
2970 CCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATATG
1 CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * *
3009 CCTTC-TAATTAGGGTAAAAGATTGGATGCTTCAATCTG
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
* * ** * * *
3047 CCTCATAACCAAGGTAAAAGATT-GATGTGTCTTCTATTTG
1 CC-CATGATCGGGGTAAGAGATTGGA-G-GT-TTCAATCTG
* * * *
3087 CCCTCTGATTGGGGTAAGAGATTGGACGACTGT-AATCTG
1 CCC-ATGATCGGGGTAAGAGATTGGA-G-GTTTCAATCTG
* * * *
3126 CCCCATGATCGGGGTAAGAGATTGGCGTGTCTTCTATTTT
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* * * * * * *
3166 CCCTTTGATTGGGTTAAGAGATTTGACGACTGT-AATTTG
1 CCC-ATGATCGGGGTAAGAGATTGGA-G-GTTTCAATCTG
* *
3205 CCCCATGATCAGGGTAAGAGATTGGTGTGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
** * ** * * * * *
3245 CCTTC-TGATTAGGGTAAAAGATCAGATGCTTAAATTTTC
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAA-TCTG
* * *
3284 CCCATGATCGGGGTAAGTGATTGGTGTGTCTTCAATCTA
1 CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
* ** * * * * *
3323 CCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATTTAC
1 CCC-ATGATCGGGGTAAGAGATTGGAGGTTTCAATCT-G
* *
3362 CCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTAT
1 CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCT-G
** ** * * * *
3402 CCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTG
1 CCCATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
** *
3439 CCCCATGATCGGGGTAAGAGATTGTTGTGTCTTCAATCTA
1 -CCCATGATCGGGGTAAGAGATTGGAG-GT-TTCAATCTG
*** * * *
3479 CCTTC-TGATTAAGGTAAAAGATTGGATGCTTCAATCTG
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
*
3517 CCCCATGATCAGGGTAAGAGATT-GATGTGTCTTCAATCTG
1 -CCCATGATCGGGGTAAGAGATTGGA-G-GT-TTCAATCTG
*** * * * *
3557 CCTTC-TGATTAAGGTAAAAGATTAGATGCTTCAATCTG
1 CC--CATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
3595 CCCCATGATCGGGGTAAGAGATTG
1 -CCCATGATCGGGGTAAGAGATTG
3619 AATGGTGATG
Statistics
Matches: 1158, Mismatches: 365, Indels: 213
0.67 0.21 0.12
Matches are distributed among these distances:
37 16 0.01
38 397 0.34
39 248 0.21
40 377 0.33
41 62 0.05
42 58 0.05
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (37 bp):
CCCATGATCGGGGTAAGAGATTGGAGGTTTCAATCTG
Found at i:2997 original size:314 final size:313
Alignment explanation
Indices: 1918--3618 Score: 1820
Period size: 314 Copynumber: 5.4 Consensus size: 313
1908 CTTGGTTTAG
* * * * **
1918 GGGTAAAAGATTGGATGGTGGCTTTAACCTGTCCCAT-ATCGGGGTAAGAGATTGGATGACATCT
1 GGGTAAAAGATTGGAT-GT---TTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCT
* * * * * * * *
1982 TCAATCTGCCC-C--ATTATCGGGTAAGAGATTGGATGGCTTCAACCTGCCCCGTGATCAGGGTA
62 TCAATCTGCCCTCTAATTA--GGGTAAAAGATTGGA-AGCTACTATCTGTCCCATGATCGGGGTA
* * * * *
2044 AAAGATTGGTGTGTTTTCAATCTAACCCTCTGATTAGGGTAAAAGATTGAATTCTTCAATCTGCC
124 AGAGATTGGTGTGTCTTCAATCT-ACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTG-C
* * * * *
2109 CCATAATCGGGGTAAGAGATTGGTGTCTCTTCAAT-TTCCCTCTGATTATGATAAAAGATCGGAT
187 CCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGAT
* * **
2173 GTTTCAATCTGCCTCATGATCAAGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
252 GCTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
* ** * * * * *
2235 GGGTAAAATATCAGATGGTTCAATATGTCCCATGATCAGGGCAAGAGATT-AAT-ATGTCTTCAA
1 GGGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCTTCAA
* * * * * *
2298 TCTGCGCTCTGATTAGGGTAAAAGA-TCGAATGCTTCTATCTGTACCATGATCGGGATAAGAGAT
66 TCTGCCCTCTAATTAGGGTAAAAGATTGGAA-GCTACTATCTGTCCCATGATCGGGGTAAGAGAT
* *
2362 TGGTGTATCTTCAATCTACCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGAT
130 TGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCC-CATGAT
* * * *
2427 TGGGGTAAGAGATTAGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGAATGCTTCTA
194 CGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAA
* * * * *
2492 TCTGCCCCATGATTGGGGTAAGAGATTGGTGTGTCTTTAATTTGCCCTCTAATTA
259 TCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
* * *
2547 GGGTAAGAGATTGGATATTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGT-TTACA
1 GGGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCTT-CA
* * * **
2611 ATCTGCCCTCTAATTAGGGTAAGAGATTGGACGGTTGTAATCTGTCCCATGATCGGGGTAAGAGA
65 ATCTGCCCTCTAATTAGGGTAAAAGATTGGAAGCTACT-ATCTGTCCCATGATCGGGGTAAGAGA
*
2676 TTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCAGATGCTTCAATCTGTCCCATGA
129 TTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTG-CCCATGA
* * *
2741 TCGGGGTAAGAGATTGGAGTGTCTTCAATCTGCCCTCTAATTAGGGTAAAAGATCGGATGCTTCA
193 TCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCA
* * * ** * *
2806 ATCTGCCTCATGATTGGGGTAAAAGATT-GAATGTCTTCAATCTGCCCTCTAATTA
258 ATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
* * * * *
2861 GGGTAAAAGATTGGTTGTTTCAATCTGCCTCGTGATCGGGGTAAGAGATTGGATGATGTTTTCAA
1 GGGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCTTCAA
* * * * * *
2926 TTTACCCTCTAATTGGGGTAAGAGATTGGACAACTACTATCTATCCCATGATCGGGGTAAGAGAT
66 TCTGCCCTCTAATTAGGGTAAAAGATTGGA-AGCTACTATCTGTCCCATGATCGGGGTAAGAGAT
* * * * * * *
2991 TGGTGTGTCTTCAATATGCCTTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCTCATAAC
130 TGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCC-CATGAT
** * * * * * * * * *
3056 CAAGGTAAAAGATTGATGTGTCTTCTATTTGCCCTCTGATTGGGGTAAGAGATTGGACGACTGT-
194 CGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATG-CT-TC
* * * * *
3120 AATCTGCCCCATGATCGGGGTAAGAGATTGGCGTGTCTTCTATTTTCCCTTTGATT-
257 AATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
* * * * *
3176 GGGTTAAGAGATTTGACGACTGT-AATTTGCCCCATGATCAGGGTAAGAGATTGG-TG-TGTCTT
1 GGG-TAAAAGATTGGATG--TTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCTT
* * ** * * *
3238 CAATCTGCCTTCTGATTAGGGTAAAAGATCAGATGCTTA-AAT-TTTCCCCATGATCGGGGTAAG
63 CAATCTGCCCTCTAATTAGGGTAAAAGATTGGAAGC-TACTATCTGT-CCCATGATCGGGGTAAG
* * * * *
3301 TGATTGGTGTGTCTTCAATCTACCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATTTACCCCA
126 AGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCT-GCCCA
* *
3366 TGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTATCCTTTGATTAGGGTAAAAGATCGGATGCT
190 TGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCT
* *
3431 TCAATCTGCCCCATGATCGGGGTAAGAGATTGTTGTGTCTTCAATCTACCTTCTGATTA
255 TCAATCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
* *
3490 AGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGATT-GATG-TGTCTTCAA
1 GGGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCTTCAA
* * * * * * * *
3553 TCTGCCTTCTGATTAAGGTAAAAGATTAGATGCTTCAATCTGCCCCATGATCGGGGTAAGAGATT
66 TCTGCCCTCTAATTAGGGTAAAAGATTGGAAGCTACTATCTGTCCCATGATCGGGGTAAGAGATT
3618 G
131 G
3619 AATGGTGATG
Statistics
Matches: 1160, Mismatches: 193, Indels: 67
0.82 0.14 0.05
Matches are distributed among these distances:
310 2 0.00
311 68 0.06
312 270 0.23
313 95 0.08
314 405 0.35
315 243 0.21
316 35 0.03
317 40 0.03
318 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (313 bp):
GGGTAAAAGATTGGATGTTTCAATCTGCCCCATGATCAGGGTAAGAGATTGGATGATGTCTTCAA
TCTGCCCTCTAATTAGGGTAAAAGATTGGAAGCTACTATCTGTCCCATGATCGGGGTAAGAGATT
GGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCATGATCG
GGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTAGGGTAAAAGATCGGATGCTTCAATC
TGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTACCCTCTGATTA
Found at i:3619 original size:78 final size:78
Alignment explanation
Indices: 1893--3618 Score: 1834
Period size: 78 Copynumber: 21.9 Consensus size: 78
1883 GAGATGATAA
* * * *
1893 CTTCAATCTGCCCCTCTTGGTTTAGGGGTAAAAGATTGGATGGTGGCTTTAACCTGTCCCAT-AT
1 CTTCAATCTG-CCCTC-T-GATTA-GGGTAAAAGATTGGA---T-GCTTCAATCTGCCCCATGAT
**
1957 CGGGGTAAGAGATTGGATGACAT
58 CGGGGTAAGAGATTGG-TG-TGT
* * * *
1980 CTTCAATCTGCCC-C--ATTATCGGGTAAGAGATTGGATGGCTTCAACCTGCCCCGTGATCAGGG
1 CTTCAATCTGCCCTCTGATTA--GGGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGGGG
*
2042 TAAAAGATTGGTGTGT
63 TAAGAGATTGGTGTGT
* * * * *
2058 TTTCAATCTAACCCTCTGATTAGGGTAAAAGATTGAATTCTTCAATCTGCCCCATAATCGGGGTA
1 CTTCAATCT-GCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTA
*
2123 AGAGATTGGTGTCT
65 AGAGATTGGTGTGT
* * * * * * **
2137 CTTCAAT-TTCCCTCTGATTATGATAAAAGATCGGATGTTTCAATCTGCCTCATGATCAAGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
2201 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * ** * * * * *
2214 CTTCAATCTACCCTCTGATTAGGGTAAAATATCAGATGGTTCAATATGTCCCATGATCAGGGCAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
** *
2279 GAGATTAATATGT
66 GAGATTGGTGTGT
* * * * ** *
2292 CTTCAATCTGCGCTCTGATTAGGGTAAAAGATCGAATGCTTCTATCTGTACCATGATCGGGATAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
2357 GAGATTGGTGTAT
66 GAGATTGGTGTGT
* * * * *
2370 CTTCAATCTACCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATTGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
2435 GAGATTAGTGTGT
66 GAGATTGGTGTGT
* * * * *
2448 CTTCAATCTACCCTCTGATTAGGGTAAAAGATCGAATGCTTCTATCTGCCCCATGATTGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
2513 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* * * * **
2526 CTTTAATTTGCCCTCTAATTAGGGTAAGAGATTGGATATTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
2591 GAGATTGGATGATGT
66 GAGATTGG-TG-TGT
* * * * * *
2606 -TTACAATCTGCCCTCTAATTAGGGTAAGAGATTGGACGGTTGTAATCTGTCCCATGATCGGGGT
1 CTT-CAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTT-CAATCTGCCCCATGATCGGGGT
2670 AAGAGATTGGTGTGT
64 AAGAGATTGGTGTGT
* ** *
2685 CTTCAATCTACCCTCTGATTAGGGTAAAAGATCAGATGCTTCAATCTGTCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
2750 GAGATTGGAGTGT
66 GAGATTGGTGTGT
* * * *
2763 CTTCAATCTGCCCTCTAATTAGGGTAAAAGATCGGATGCTTCAATCTGCCTCATGATTGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
* **
2828 AAGATT-GAATGT
66 GAGATTGGTGTGT
* * * * *
2840 CTTCAATCTGCCCTCTAATTAGGGTAAAAGATTGGTTGTTTCAATCTGCCTCGTGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
2905 GAGATTGGATGATGT
66 GAGATTGG-TG-TGT
* * * * * * ** * * **
2920 TTTCAATTTACCCTCTAATTGGGGTAAGAGATTGGACAACTACTATCTATCCCATGATCGGGGTA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGA-TGCTTCAATCTGCCCCATGATCGGGGTA
2985 AGAGATTGGTGTGT
65 AGAGATTGGTGTGT
* * * * * * **
2999 CTTCAATATGCCTTCTAATTAGGGTAAAAGATTGGATGCTTCAATCTGCCTCATAACCAAGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
* *
3064 AAGATTGATGTGT
66 GAGATTGGTGTGT
* * * * *
3077 CTTCTATTTGCCCTCTGATTGGGGTAAGAGATTGGACGACTGT-AATCTGCCCCATGATCGGGGT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATG-CT-TCAATCTGCCCCATGATCGGGGT
*
3141 AAGAGATTGGCGTGT
64 AAGAGATTGGTGTGT
* * * * * * * * *
3156 CTTCTATTTTCCCTTTGATT-GGGTTAAGAGATTTGACGACTGT-AATTTGCCCCATGATCAGGG
1 CTTCAATCTGCCCTCTGATTAGGG-TAAAAGATTGGATG-CT-TCAATCTGCCCCATGATCGGGG
3219 TAAGAGATTGGTGTGT
63 TAAGAGATTGGTGTGT
* ** * * *
3235 CTTCAATCTGCCTTCTGATTAGGGTAAAAGATCAGATGCTTAAATTTTCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
3300 GTGATTGGTGTGT
66 GAGATTGGTGTGT
* * * *
3313 CTTCAATCTACCCTTTGATTAGGGTAAAAGATTGGATGCTTCAATTTACCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
3378 GAGATTGGTGTGT
66 GAGATTGGTGTGT
** * *
3391 CTTCAATCTATCCTTTGATTAGGGTAAAAGATCGGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
3456 GAGATTGTTGTGT
66 GAGATTGGTGTGT
* * * *
3469 CTTCAATCTACCTTCTGATTAAGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCAGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
*
3534 GAGATTGATGTGT
66 GAGATTGGTGTGT
* * *
3547 CTTCAATCTGCCTTCTGATTAAGGTAAAAGATTAGATGCTTCAATCTGCCCCATGATCGGGGTAA
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
3612 GAGATTG
66 GAGATTG
3619 AATGGTGATG
Statistics
Matches: 1404, Mismatches: 214, Indels: 51
0.84 0.13 0.03
Matches are distributed among these distances:
77 135 0.10
78 810 0.58
79 256 0.18
80 110 0.08
81 61 0.04
82 18 0.01
85 1 0.00
86 3 0.00
87 10 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (78 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCGGGGTAA
GAGATTGGTGTGT
Found at i:4001 original size:98 final size:99
Alignment explanation
Indices: 3856--4304 Score: 297
Period size: 99 Copynumber: 4.6 Consensus size: 99
3846 CTCGTCATGT
* * * * * **
3856 TTCTAAGGTACTAGGTTCGTTGTTGTGACCTCAACCTTTCCCTTTATAT-TTCCATGGTATTG-G
1 TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTATATCTT-CATGGTACCGAG
** *
3919 ATTCGCCATTGTGGTCTCAATCC-TCCCATCACATC
65 -TTCGCCATTACGGCCTCAATCCTTCCCATCACATC
*
3954 TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCTCATTATATCTTCATGGTACCGAGT
1 TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTATATCTTCATGGTACCGAGT
*
4019 TCGCCGTTACGGCCTCAATCCTTCCCATCACATC
66 TCGCCATTACGGCCTCAATCCTTCCCATCACATC
* * * * * * *
4053 TTCTAAGGTACCGAGTTTGCCATTGCGGCCTCAACCTTTCCC-TTCAAATCTCCATGGTACC-AG
1 TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATT-ATATCTTCATGGTACCGAG
* * * **
4116 ATTCGCCTTTGCAGCCTCAA-CCTTTCCCATTTCAT-
65 -TTCGCCATTACGGCCTCAATCC-TTCCCATCACATC
* ** ** **** * * * * * *
4151 TT-TATGGTACTGATTTCGTTATTATAACCTCAATCTTTCCCATCATGTCTTCTTAGGTATCGGG
1 TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTATATCTTCAT-GGTACCGAG
* * * *
4215 TTCGCCATTGCGACCTCAA-CCTTTCCCTTCAAATC
65 TTCGCCATTACGGCCTCAATCC-TTCCCATCACATC
* * * * * * * * *
4250 -TCCATGGTACCGAGTTCGCCATTGTGGCCTCTACCTTTCCCTTTATATCTTCATG
1 TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTATATCTTCATG
4305 TTTCCTAGGT
Statistics
Matches: 276, Mismatches: 64, Indels: 22
0.76 0.18 0.06
Matches are distributed among these distances:
97 34 0.12
98 112 0.41
99 130 0.47
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (99 bp):
TTCTAAGGTACTGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATTATATCTTCATGGTACCGAGT
TCGCCATTACGGCCTCAATCCTTCCCATCACATC
Found at i:4013 original size:49 final size:49
Alignment explanation
Indices: 3884--4304 Score: 248
Period size: 49 Copynumber: 8.6 Consensus size: 49
3874 GTTGTTGTGA
* * * *
3884 CCTCAACCTTTCCCTTTATAT-TTCCATGGTATTGGATTCGCCATTGTGG
1 CCTCAACCTTTCCCATTATATCTT-CATGGTACTGGGTTCGCCATTGCGG
* * * * * *
3933 TCTCAATCC--TCCCATCACATCTTCTAAGGTACTGGGTTCGTCGTTGCGG
1 CCTCAA-CCTTTCCCATTATATCTTC-ATGGTACTGGGTTCGCCATTGCGG
* * * * *
3982 CCTCAACCTTTCTCATTATATCTTCATGGTACCGAGTTCGCCGTTACGG
1 CCTCAACCTTTCCCATTATATCTTCATGGTACTGGGTTCGCCATTGCGG
* * * * * *
4031 CCTCAATCC-TTCCCATCACATCTTCTAAGGTACCGAGTTTGCCATTGCGG
1 CCTCAA-CCTTTCCCATTATATCTTC-ATGGTACTGGGTTCGCCATTGCGG
* * ** * * *
4081 CCTCAACCTTTCCC-TTCAAATCTCCATGGTACCAGATTCGCCTTTGCAG
1 CCTCAACCTTTCCCATT-ATATCTTCATGGTACTGGGTTCGCCATTGCGG
* ** ** ****
4130 CCTCAACCTTTCCCATT-TCAT-TTTATGGTACTGATTTCGTTATTATAA
1 CCTCAACCTTTCCCATTAT-ATCTTCATGGTACTGGGTTCGCCATTGCGG
* * * * *
4178 CCTCAATCTTTCCCATCATGTCTTCTTAGGTA-TCGGGTTCGCCATTGCGA
1 CCTCAACCTTTCCCATTATATCTTCAT-GGTACT-GGGTTCGCCATTGCGG
* * * * *
4228 CCTCAACCTTTCCC-TTCAAATCTCCATGGTACCGAGTTCGCCATTGTGG
1 CCTCAACCTTTCCCATT-ATATCTTCATGGTACTGGGTTCGCCATTGCGG
* *
4277 CCTCTACCTTTCCCTTTATATCTTCATG
1 CCTCAACCTTTCCCATTATATCTTCATG
4305 TTTCCTAGGT
Statistics
Matches: 280, Mismatches: 74, Indels: 36
0.72 0.19 0.09
Matches are distributed among these distances:
48 42 0.15
49 149 0.53
50 89 0.32
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (49 bp):
CCTCAACCTTTCCCATTATATCTTCATGGTACTGGGTTCGCCATTGCGG
Found at i:4966 original size:112 final size:110
Alignment explanation
Indices: 4725--5054 Score: 342
Period size: 112 Copynumber: 2.9 Consensus size: 110
4715 TCTTATATTC
* * * *
4725 TTAGACCACTAACCGTCATTGCAATGA-AAAATGCTTGAACAGGGTTGTAAGGTAGATAAAATTG
1 TTAGTCCACTAACCGTTATTTCAAT-ACAAAATGCTTGAACA-GGTTGTAAGGTGGATAAAATTG
* * *
4789 AATTTTATTGGAGGTAAGGCTC--ACGTGAATGAAAAGATTAAGAATCA
64 AATTTTATTAGAGGTAAAGCTCGTAC--GAATGAAAAGGTTAAGAATCA
* * * * * **
4836 TTAGTCTAGTGACTGTTATTTCAATACAAACGTGCTTGAACATGGTTGTAAGGTGGATAAAATAA
1 TTAGTCCACTAACCGTTATTTCAATACAAA-ATGCTTGAACA-GGTTGTAAGGTGGATAAAATTG
*
4901 AATTTCATTAGAGGTAAAGCTCGTACGAATGAAAAGGTTAAGAATCA
64 AATTTTATTAGAGGTAAAGCTCGTACGAATGAAAAGGTTAAGAATCA
* * * *
4948 TTGGTCCACTAACCGTTATTTCGATGCAAAAATGCTTGAACCAGGTTGTAAGGTGGATAAATTTG
1 TTAGTCCACTAACCGTTATTTCAATAC-AAAATGCTTGAA-CAGGTTGTAAGGTGGATAAAATTG
* ** * *
5013 ACTTTTATTTTAGGCAAAGCTCGTATGAATGAAAAGGATTAA
64 AATTTTATTAGAGGTAAAGCTCGTACGAATGAAAAGG-TTAA
5055 ATTTACCTAT
Statistics
Matches: 179, Mismatches: 33, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
110 1 0.01
111 21 0.12
112 146 0.82
113 9 0.05
114 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (110 bp):
TTAGTCCACTAACCGTTATTTCAATACAAAATGCTTGAACAGGTTGTAAGGTGGATAAAATTGAA
TTTTATTAGAGGTAAAGCTCGTACGAATGAAAAGGTTAAGAATCA
Done.