Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001535.1 Kokia drynarioides strain JFW-HI SEQ_113105, 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: 20163
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Found at i:269 original size:17 final size:17
Alignment explanation
Indices: 247--318 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
237 TATTTCAAAT
*
247 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
264 TTTAAACTT--AATAAA
1 TTTAAACTTAAAATAAA
*
279 TTTAAATTTAAAAT-AA
1 TTTAAACTTAAAATAAA
*
295 TTCTAAACTTAGAATAAA
1 TT-TAAACTTAAAATAAA
313 TTTAAA
1 TTTAAA
319 ATAAAGATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
15 14 0.30
16 4 0.09
17 25 0.53
18 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:285 original size:32 final size:33
Alignment explanation
Indices: 247--318 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
237 TATTTCAAAT
247 TTTAAATTTAAAATAAATT-TAAACTT-AATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTTAAATAAA
279 TTTAAATTTAAAATAATTCTAAACTTAGAATAAA
1 TTTAAATTTAAAATAATTCTAAACTTA-AATAAA
313 TTTAAA
1 TTTAAA
319 ATAAAGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
31 4 0.11
32 21 0.57
34 12 0.32
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (33 bp):
TTTAAATTTAAAATAATTCTAAACTTAAATAAA
Found at i:1100 original size:49 final size:48
Alignment explanation
Indices: 983--1853 Score: 529
Period size: 49 Copynumber: 17.8 Consensus size: 48
973 TAAGGTATGA
* * * ** * * *
983 GGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGCCT-TCGTGGCACT
1 GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCT-GAGGTACT
* * * *
1031 GGATTCACCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCT
1 GG-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* * * * *
1080 AGGTTCGTCGTTGCGACTTAAACCTTTCCCTT-TTGTATCTTTGAGGTACT
1 -GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG--TCTCTGAGGTACT
* * * * * *
1130 AGATCTGCTGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACAA
1 GGTTC-GCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAC-T
* * * ** * *
1180 GGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACT
1 GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* * * * * *
1228 GCATCCACCGTTGCGGCTTAGATCTTTCCCTTCATG-CTTCTAAGGTACAA
1 G-GTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTAC-T
* * * * * * * *
1278 GGTTCGTCATGGTGACTTAAA-CGTTTCCCTTTC-TATCTTTGTGGTACT
1 GGTTCGCCGTTGCGGCTTAAATC-TTTCCC-TTCATGTCTCTGAGGTACT
* *
1326 GGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCT
1 GG-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* * * * * * *
1375 AGGTTCGTCATTGCGACTTAAACCTTTCCCTT-TTGTATCTTTGCGGTACT
1 -GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG--TCTCTGAGGTACT
* * * *
1425 GGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACAA
1 GG-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTAC-T
** * * * ** * *
1475 GGTTTACTGTTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACT
1 GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* * * *
1523 GGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCATG-CTTCAGAGGTACAA
1 GGTTC-GCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTAC-T
* ** * * * ** *
1573 GGTTCACCGTTGCAACTTAAACCTTTTCGTTTGTGTCT-TTATGGTACT
1 GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGA-GGTACT
* * * *
1621 GGATC-CATCGTTGCGGCTTAGATCTTTCCCTTTATGTCTCTGTGGTACT
1 GGTTCGC--CGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* *
1670 GGATTCACCGTTGCGGCTTACATCTTTCCCTTCATGTCTCTGAGGTACT
1 GG-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* * * * ** * *
1719 AGGCTCGTCGTTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACT
1 -GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
* * * * *
1768 GGATCCGTCGTTGCGGCTTAGATCTTTCCCTTCATG-CTTCTGTGATACT
1 GG-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACT
1817 GGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT
1 GG-TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGT
1854 TTTGTGGTAC
Statistics
Matches: 608, Mismatches: 178, Indels: 72
0.71 0.21 0.08
Matches are distributed among these distances:
47 1 0.00
48 26 0.04
49 485 0.80
50 91 0.15
51 5 0.01
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (48 bp):
GGTTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACT
Found at i:1105 original size:98 final size:98
Alignment explanation
Indices: 982--1853 Score: 828
Period size: 98 Copynumber: 8.9 Consensus size: 98
972 TTAAGGTATG
* * * * * * * *
982 AGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGCCTTCGTGGCACTGGATTCACCGTTACAG
1 AGGTTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATTCGCCGTTGCGG
* * *
1047 CTTAAATCTTTCCCTTCATGTCTCTGAGGTTCT
66 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
* * * * *
1080 AGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTGTATCTTTGAGGTACTAGA-TCTGCTGTTGC
1 AGGTTCGTCATTGCGACTTAAACCTTTCCC-TTTGTGTCTTTGCGGTACTGGATTC-GCCGTTGC
*
1144 GGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACA
64 GGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
* * * *
1179 AGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGCATCCACCGTTGCGG
1 AGGTTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATTCGCCGTTGCGG
*
1244 CTTAGATCTTTCCCTTCATG-CTTCTAAGGTACA
66 CTTAGATCTTTCCCTTCATGTC-TCTGAGGTACA
* * * * * * *
1277 AGGTTCGTCATGGTGACTTAAACGTTTCCCTTTCTATCTTTGTGGTACTGGATTCGCCGTTACGG
1 AGGTTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATTCGCCGTTGCGG
* * *
1342 CTTAAATCTTTCCCTTCATGTCTCTGAGGTTCT
66 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
* *
1375 AGGTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTGCG
1 AGGTTCGTCATTGCGACTTAAACCTTTCCC-TTTGTGTCTTTGCGGTACTGGATTCGCCGTTGCG
*
1440 GCTTAGATCTTTCCCTTCATGTCTCTAAGGTACA
65 GCTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
* *
1474 AGGTT--TACTGTTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACTGGA-TCTGCCGTTG
1 AGGTTCGT-C-ATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATTC-GCCGTTG
*
1536 CGGCTTAGATCTTTCCCTTCATG-CTTCAGAGGTACA
63 CGGCTTAGATCTTTCCCTTCATGTC-TCTGAGGTACA
** * * * * ** * **
1572 AGGTTCACCGTTGCAACTTAAACCTTTTCGTTTGTGTCTTTATGGTACTGGATCCATCGTTGCGG
1 AGGTTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATTCGCCGTTGCGG
* *
1637 CTTAGATCTTTCCCTTTATGTCTCTGTGGTAC-
66 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
* ** * * * * ** * * * *
1669 TGGATTCACCGTTGCGGCTTACATCTTTCCCTTCATGTCTCTGAGGTACTAGG-CTCGTCGTTGC
1 AGG-TTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACT-GGATTCGCCGTTGC
* * * ** * *
1733 GACTTAAACCTTTCCCTTTGTGTCTTTGCGGTAC-
64 GGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
* * * * * * ** * *
1767 TGGATCCGTCGTTGCGGCTTAGATCTTTCCCTTCATG-CTTCTGTGATACTGGATTCGCCGTTGC
1 AGG-TTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTT-TGCGGTACTGGATTCGCCGTTGC
*
1831 GGCTTAAATCTTTCCCTTCATGT
64 GGCTTAGATCTTTCCCTTCATGT
1854 TTTGTGGTAC
Statistics
Matches: 652, Mismatches: 104, Indels: 36
0.82 0.13 0.05
Matches are distributed among these distances:
97 10 0.02
98 471 0.72
99 171 0.26
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (98 bp):
AGGTTCGTCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATTCGCCGTTGCGG
CTTAGATCTTTCCCTTCATGTCTCTGAGGTACA
Found at i:1308 original size:197 final size:196
Alignment explanation
Indices: 973--1661 Score: 870
Period size: 197 Copynumber: 3.5 Consensus size: 196
963 TTTATGTTTT
** * * * * *
973 TAAGGTATGAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGCCTTCGTGGCACTGGATTCA
1 TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATCCA
* * * * * * * *
1038 CCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGGTTCGTCGTTGCGACTTAAAC
66 CCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACAAGGTTCGTCATGGCGACTTAAAC
* *
1103 CTTTCCCTTTTGTATCTTTGAGGTACTAGATCTGCTGTTGCGGCTTAGATCTTTCCCTTCATGTC
131 CTTTCCC-TTTGTATCTTTGAGGTACTGGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC
1168 TC
195 TC
*
1170 TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGCATCCA
1 TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATCCA
*
1235 CCGTTGCGGCTTAGATCTTTCCCTTCATG-CTTCTAAGGTACAAGGTTCGTCATGGTGACTTAAA
66 CCGTTGCGGCTTAGATCTTTCCCTTCATGTC-TCTAAGGTACAAGGTTCGTCATGGCGACTTAAA
* * * * *
1299 CGTTTCCCTTTCTATCTTTGTGGTACTGGAT-TCGCCGTTACGGCTTAAATCTTTCCCTTCATGT
130 CCTTTCCCTTTGTATCTTTGAGGTACTGGATCT-GCCGTTGCGGCTTAGATCTTTCCCTTCATGT
1363 CTC
194 CTC
* * * * *
1366 TGAGGTTCTAGGTTCGTCATTGCGACTTAAACCTTTCCCTTTTGTATCTTTGCGGTACTGGATCC
1 TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCC-TTTGTGTCTTTGCGGTACTGGATCC
*
1431 GCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACAAGGTT--T-ACTGTTGCGACTT
65 ACCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACAAGGTTCGTCA-TG--GCGACTT
* * *
1493 AAACCTTTCCCTTTGTGTCTATGCGGTACTGGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCAT
127 AAACCTTTCCCTTTGTATCTTTGAGGTACTGGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCAT
1558 G-CT-
192 GTCTC
* * * * * **
1561 TCAGAGGTACAAGGTTCACCGTTGCAACTTAAACCTTTTCGTTTGTGTCTTTATGGTACTGGATC
1 T-A-AGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATC
* *
1626 CATCGTTGCGGCTTAGATCTTTCCCTTTATGTCTCT
64 CACCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCT
1662 GTGGTACTGG
Statistics
Matches: 428, Mismatches: 54, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
194 1 0.00
195 5 0.01
196 143 0.33
197 277 0.65
198 2 0.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (196 bp):
TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATCCA
CCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTAAGGTACAAGGTTCGTCATGGCGACTTAAAC
CTTTCCCTTTGTATCTTTGAGGTACTGGATCTGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCT
C
Found at i:1353 original size:147 final size:147
Alignment explanation
Indices: 973--1853 Score: 613
Period size: 147 Copynumber: 6.0 Consensus size: 147
963 TTTATGTTTT
** * * * ** * *
973 TAAGGTATGAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGCCTTCGTGGCACTGGATTCA
1 TAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTCTGTCTTTATGGTACTGGATCCA
* * * * * * *
1038 CCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGG-TTCGTCGTTGCGACTTAAA
66 CCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGCGGTACT-GGATTCGCCGTTGCGGCTTAAA
* *
1102 CCTTTCCCTT-TTGTATC
130 TCTTTCCCTTCATGTATC
* * * * * * * * * *
1119 TTTGAGGTACTA-GATCTGCTGTTGCGGCTTAGATCTTTCCC-TTCATGTCTCTAAGGTACAAGG
1 --TAAGGTACAAGGTTC-GCCGTTGCGACTTAAACCTTTCCCTTTC-TGTCTTTATGGTAC-TGG
* * * * * * * * * *
1182 -TTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGCATCCACCGTTGCGGCT
61 ATCCACCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGCGGTACTGGATTCGCCGTTGCGGCT
*
1246 TAGATCTTTCCCTTCATGCT-TC
126 TAAATCTTTCCCTTCATG-TATC
* * * * * * * * *
1268 TAAGGTACAAGGTTCGTCATGGTGACTTAAACGTTTCCCTTTCTATCTTTGTGGTACTGGATTCG
1 TAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTCTGTCTTTATGGTACTGGATCCA
* * * * * * *
1333 CCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGG-TTCGTCATTGCGACTTAAA
66 CCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGCGGTACT-GGATTCGCCGTTGCGGCTTAAA
* *
1397 CCTTTCCCTT-TTGTATC
130 TCTTTCCCTTCATGTATC
** * * * * * * * *
1414 TTTGCGGTAC-TGGATCCGCCGTTGCGGCTTAGATCTTTCCC-TTCATGTCTCTAAGGTACAAGG
1 --TAAGGTACAAGG-TTCGCCGTTGCGACTTAAACCTTTCCCTTTC-TGTCTTTATGGTAC-TGG
** * * * * *
1477 -TTTACTGTTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACTGGA-TCTGCCGTTGCGGC
61 ATCCACCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGCGGTACTGGATTC-GCCGTTGCGGC
*
1540 TTAGATCTTTCCCTTCATGCT-TC
125 TTAAATCTTTCCCTTCATG-TATC
* * * * *
1563 -AGAGGTACAAGGTTCACCGTTGCAACTTAAACCTTTTCGTTTGTGTCTTTATGGTACTGGATCC
1 TA-AGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTCTGTCTTTATGGTACTGGATCC
* * * * *
1627 ATCGTTGCGGCTTAGATCTTTCCCTTTATGTCTCTGTGGTACTGGATTCACCGTTGCGGCTTACA
65 ACCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGCGGTACTGGATTCGCCGTTGCGGCTTAAA
*
1692 TCTTTCCCTTCATGTCTC
130 TCTTTCCCTTCATGTATC
* * * * * ** *
1710 TGAGGTACTAGGCTCGTCGTTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGGATCCG
1 TAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTCTGTCTTTATGGTACTGGATCCA
* * * * *
1775 TCGTTGCGGCTTAGATCTTTCCCTTCATG-CTTCTGTGATACTGGATTCGCCGTTGCGGCTTAAA
66 CCGTTGCGGCTTAAATCTTTCCCTTTATGTC-TCTGCGGTACTGGATTCGCCGTTGCGGCTTAAA
1839 TCTTTCCCTTCATGT
130 TCTTTCCCTTCATGT
1854 TTTGTGGTAC
Statistics
Matches: 558, Mismatches: 147, Indels: 57
0.73 0.19 0.07
Matches are distributed among these distances:
145 1 0.00
146 10 0.02
147 338 0.61
148 195 0.35
149 12 0.02
150 2 0.00
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (147 bp):
TAAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTTCTGTCTTTATGGTACTGGATCCA
CCGTTGCGGCTTAAATCTTTCCCTTTATGTCTCTGCGGTACTGGATTCGCCGTTGCGGCTTAAAT
CTTTCCCTTCATGTATC
Found at i:1701 original size:295 final size:295
Alignment explanation
Indices: 973--1662 Score: 1031
Period size: 295 Copynumber: 2.3 Consensus size: 295
963 TTTATGTTTT
** * * *
973 TAAGGTATGAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGCCTTCGTGGCACTGGATTCA
1 TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCA
*
1038 CCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGGTTCGTCGTTGCGACTTAAAC
66 CCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGGTTCGTCGTTGCGACTTAAAC
* *
1103 CTTTCCCTTTTGTATCTTTGAGGTACTAGATCTGCTGTTGCGGCTTAGATCTTTCCCTTCATGTC
131 CTTTCCCTTTTGTATCTTTGAGGTACTAGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC
* *
1168 TCTAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGCGGTACTGCATC
196 TCTAAGGTACAAGGTTCACCATTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACTGCATC
1233 CACCGTTGCGGCTTAGATCTTTCCCTTCATGCTTC
261 CACCGTTGCGGCTTAGATCTTTCCCTTCATGCTTC
* * * * * * *
1268 TAAGGTACAAGGTTCGTCATGGTGACTTAAACGTTTCCCTTTCTATCTTTGTGGTACTGGATTCG
1 TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCA
*
1333 CCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGGTTCGTCATTGCGACTTAAAC
66 CCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGGTTCGTCGTTGCGACTTAAAC
* *
1398 CTTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC
131 CTTTCCCTTTTGTATCTTTGAGGTACTAGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC
* ** *
1463 TCTAAGGTACAAGGTTTACTGTTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACTGGATC
196 TCTAAGGTACAAGGTTCACCATTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACTGCATC
**
1528 TGCCGTTGCGGCTTAGATCTTTCCCTTCATGCTTC
261 CACCGTTGCGGCTTAGATCTTTCCCTTCATGCTTC
* * * * * * *
1563 -AGAGGTACAAGGTTCACCGTTGCAACTTAAACCTTTTCGTTTGTGTCTTTATGGTACTGGATCC
1 TA-AGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTC
* * * *
1627 ATCGTTGCGGCTTAGATCTTTCCCTTTATGTCTCTG
65 ACCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTG
1663 TGGTACTGGA
Statistics
Matches: 350, Mismatches: 44, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
294 1 0.00
295 349 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (295 bp):
TAAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTTGTGGTACTGGATTCA
CCGTTACGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTTCTAGGTTCGTCGTTGCGACTTAAAC
CTTTCCCTTTTGTATCTTTGAGGTACTAGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTC
TCTAAGGTACAAGGTTCACCATTGCGACTTAAACCTTTCCCTTTGTGTCTATGCGGTACTGCATC
CACCGTTGCGGCTTAGATCTTTCCCTTCATGCTTC
Found at i:6550 original size:19 final size:19
Alignment explanation
Indices: 6507--6548 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
6497 GCCAGTCGTG
6507 CTTTTCTCATCTCTTGCTT
1 CTTTTCTCATCTCTTGCTT
* *
6526 CTTTTC-CATCTTTTTCTT
1 CTTTTCTCATCTCTTGCTT
6544 CTTTT
1 CTTTT
6549 TCTTCATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.05, C:0.29, G:0.02, T:0.64
Consensus pattern (19 bp):
CTTTTCTCATCTCTTGCTT
Found at i:13163 original size:96 final size:96
Alignment explanation
Indices: 12989--13181 Score: 266
Period size: 96 Copynumber: 2.0 Consensus size: 96
12979 AATTTTGGAA
*
12989 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGTAATTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTC-TAACTAGTAAGTTAAGGCACAAATTTTCA
* *
13054 GAATCAGAGATAAAA-AACATTGCCTCGATTT
65 AAATCAGAAATAAAAGAACATTGCCTCGATTT
* * *
13085 AAGGGTATTCGATTATTTCGATTTGAGGAAAAGT-TACACCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCTA-A-CTAGTAAGTTAAGGCACAAATTTTC
*
13149 AAAACTC-GAAATAAAAGAATATTGCCTCGATTT
64 AAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
13182 TAAAGTTTTC
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
94 2 0.02
95 1 0.01
96 66 0.77
97 17 0.20
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCTAACTAGTAAGTTAAGGCACAAATTTTCAA
AATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:13431 original size:28 final size:28
Alignment explanation
Indices: 13400--13459 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
13390 AAAATGAGAT
* *
13400 TTTTGGATACAGGGGGGCAAAATGGTAA
1 TTTTGGACACACGGGGGCAAAATGGTAA
**
13428 TTTTGGACATTCGGGGGCAAAATGGTAA
1 TTTTGGACACACGGGGGCAAAATGGTAA
13456 TTTT
1 TTTT
13460 AGGAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.32, T:0.32
Consensus pattern (28 bp):
TTTTGGACACACGGGGGCAAAATGGTAA
Found at i:13587 original size:29 final size:28
Alignment explanation
Indices: 13555--13727 Score: 138
Period size: 29 Copynumber: 6.0 Consensus size: 28
13545 ATTTTTAGAT
13555 AATTGGGGGTAAAATGGTAATTTTGGAAA
1 AATTGGGGGTAAAATGGTAATTTTGG-AA
***
13584 AATT-TAAGTCAAAAATGG-AATTTTTGGAA
1 AATTGGGGGT--AAAATGGTAA-TTTTGGAA
* *
13613 GATTAGGGGTAAAATGGTAATTTTGGAA
1 AATTGGGGGTAAAATGGTAATTTTGGAA
* * *
13641 AATTCGGGGTTGAAAAT-GAAATTTTTGAA
1 AATT-GGGGGT-AAAATGGTAATTTTGGAA
* *
13670 AGTTCGAGGGTAAAATGGTAATTTTGGAAA
1 AATT-GGGGGTAAAATGGTAATTTTGG-AA
* *
13700 AATTAGGGTTAAAATGG-AATTTTGGAA
1 AATTGGGGGTAAAATGGTAATTTTGGAA
13727 A
1 A
13728 GTTCGAGGGA
Statistics
Matches: 114, Mismatches: 21, Indels: 20
0.74 0.14 0.13
Matches are distributed among these distances:
27 3 0.03
28 33 0.29
29 53 0.46
30 25 0.22
ACGTcount: A:0.39, C:0.02, G:0.27, T:0.32
Consensus pattern (28 bp):
AATTGGGGGTAAAATGGTAATTTTGGAA
Found at i:13709 original size:58 final size:56
Alignment explanation
Indices: 13497--13741 Score: 230
Period size: 58 Copynumber: 4.2 Consensus size: 56
13487 TTTCTAGACA
* *
13497 TTCGAGGGTAAAATGGTAATTTTTAGG-AAGTTCGGGATTTAAAATGAAATTTTTAGATAA-
1 TTCGAGGGTAAAATGGTAA-TTTT-GGAAAATTAGGG--TTAAAATGAAATTTTT-GA-AAG
* * * * *
13557 TT-GGGGGTAAAATGGTAATTTTGGAAAAATTTA-AGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTGG-AAAA-TTAGGGT-TAAAATGAAATTTTTGAAAG
* *
13614 ATTAG-GGGTAAAATGGTAATTTTGGAAAATTCGGGGTTGAAAATGAAATTTTTGAAAG
1 -TTCGAGGGTAAAATGGTAATTTTGGAAAATT-AGGGTT-AAAATGAAATTTTTGAAAG
* *
13672 TTCGAGGGTAAAATGGTAATTTTGGAAAAATTAGGGTTAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTGG-AAAATTAGGGTTAAAATGAAATTTTTGAAAG
*
13729 TTCGAGGGAAAAA
1 TTCGAGGGTAAAA
13742 ACATAATTTT
Statistics
Matches: 156, Mismatches: 17, Indels: 27
0.78 0.09 0.14
Matches are distributed among these distances:
56 4 0.03
57 40 0.26
58 83 0.53
59 25 0.16
60 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (56 bp):
TTCGAGGGTAAAATGGTAATTTTGGAAAATTAGGGTTAAAATGAAATTTTTGAAAG
Found at i:13741 original size:28 final size:28
Alignment explanation
Indices: 13418--13741 Score: 141
Period size: 28 Copynumber: 11.1 Consensus size: 28
13408 ACAGGGGGGC
* * *
13418 AAAATGGTAATTTTGGACA-TTCGGGGGC
1 AAAATGG-AATTTTGGAAAGTTCGAGGGT
*
13446 AAAATGGTAATTTTAGGAAAGTTC-AAGGT
1 AAAATGG-AATTTT-GGAAAGTTCGAGGGT
* * *
13475 AAAAAAACGGAATTTCTAGACA-TTCGAGGGT
1 ---AAAATGGAATTT-TGGAAAGTTCGAGGGT
*
13506 AAAATGGTAATTTTTAGG-AAGTTCG-GGATTT
1 AAAATGG-AA-TTTT-GGAAAGTTCGAGG--GT
* * *
13537 AAAATGAAATTTTTAGATAA-TT-GGGGGT
1 AAAATGGAA-TTTTGGA-AAGTTCGAGGGT
* ** ***
13565 AAAATGGTAATTTTGGAAAAATTTAAGTCA
1 AAAATGG-AATTTTGG-AAAGTTCGAGGGT
*
13595 AAAATGGAATTTTTGG-AAGATTAG-GGGT
1 AAAATGGAA-TTTTGGAAAG-TTCGAGGGT
*
13623 AAAATGGTAATTTTGGAAAATTCG-GGGTT
1 AAAATGG-AATTTTGGAAAGTTCGAGGG-T
* *
13652 GAAAATGAAATTTTTGAAAGTTCGAGGGT
1 -AAAATGGAATTTTGGAAAGTTCGAGGGT
*
13681 AAAATGGTAATTTTGGAAAAATT--AGGGTT
1 AAAATGG-AATTTTGG-AAAGTTCGAGGG-T
*
13710 AAAATGGAATTTTGGAAAGTTCGAGGGA
1 AAAATGGAATTTTGGAAAGTTCGAGGGT
13738 AAAA
1 AAAA
13742 ACATAATTTT
Statistics
Matches: 226, Mismatches: 38, Indels: 64
0.69 0.12 0.20
Matches are distributed among these distances:
27 5 0.02
28 78 0.35
29 62 0.27
30 53 0.23
31 21 0.09
32 7 0.03
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:13749 original size:57 final size:58
Alignment explanation
Indices: 13630--13751 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 58
13620 GGTAAAATGG
* * * ***
13630 TAATTTTGGAAAATTCGGGGTTGAAAATGAAATTTTTGAAAGTTCGAGGGTAAAATGG
1 TAATTTTGGAAAATTCAGGGTTGAAAATGAAATTTTGGAAAGTTCGAGGGAAAAAACA
*
13688 TAATTTTGGAAAAATT-AGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGAAAAAACA
1 TAATTTTGG-AAAATTCAGGGTTGAAAATGAAATTTTGGAAAGTTCGAGGGAAAAAACA
13745 TAATTTT
1 TAATTTT
13752 TGGATAGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
57 36 0.64
58 14 0.25
59 6 0.11
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (58 bp):
TAATTTTGGAAAATTCAGGGTTGAAAATGAAATTTTGGAAAGTTCGAGGGAAAAAACA
Found at i:14717 original size:3 final size:3
Alignment explanation
Indices: 14711--14784 Score: 103
Period size: 3 Copynumber: 24.0 Consensus size: 3
14701 CTTTTTTTAT
* * *
14711 TTA TTA TTA ATA TTTA TTA TTA ATA TTG TTA TTAA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
14758 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
14785 ATGAAATTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
3 58 0.92
4 5 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:15631 original size:17 final size:17
Alignment explanation
Indices: 15609--15680 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
15599 TATTTCAAAT
*
15609 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
15626 TTTAAACTT--AATAAA
1 TTTAAACTTAAAATAAA
**
15641 TTTAAGTTTAAAAT-AA
1 TTTAAACTTAAAATAAA
*
15657 TTCTAAACTTAGAATAAA
1 TT-TAAACTTAAAATAAA
15675 TTTAAA
1 TTTAAA
15681 ATAAAGATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.29
16 4 0.09
17 24 0.53
18 4 0.09
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:15651 original size:32 final size:33
Alignment explanation
Indices: 15609--15680 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
15599 TATTTCAAAT
15609 TTTAAATTTAAAATAAATT-TAAACTT-AATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTTAAATAAA
*
15641 TTTAAGTTTAAAATAATTCTAAACTTAGAATAAA
1 TTTAAATTTAAAATAATTCTAAACTTA-AATAAA
15675 TTTAAA
1 TTTAAA
15681 ATAAAGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 4 0.11
32 20 0.57
34 11 0.31
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (33 bp):
TTTAAATTTAAAATAATTCTAAACTTAAATAAA
Found at i:16585 original size:24 final size:24
Alignment explanation
Indices: 16558--16607 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
16548 GTTATTGGAT
*
16558 TAATGATTTAATATAAATAAATAA
1 TAATGATTTAACATAAATAAATAA
* * *
16582 TAATTATTTAACATATATAATTAA
1 TAATGATTTAACATAAATAAATAA
16606 TA
1 TA
16608 TAATTATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (24 bp):
TAATGATTTAACATAAATAAATAA
Found at i:17236 original size:18 final size:16
Alignment explanation
Indices: 17201--17233 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17191 ATTCAATATT
17201 ATATATTATATTAAAA
1 ATATATTATATTAAAA
*
17217 ATATTTTATATTAAAA
1 ATATATTATATTAAAA
17233 A
1 A
17234 AATTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATTATATTAAAA
Found at i:17238 original size:16 final size:16
Alignment explanation
Indices: 17206--17238 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17196 ATATTATATA
*
17206 TTATATTAAAAATATT
1 TTATATTAAAAAAATT
17222 TTATATTAAAAAAATT
1 TTATATTAAAAAAATT
17238 T
1 T
17239 CTTTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATTAAAAAAATT
Found at i:18744 original size:21 final size:22
Alignment explanation
Indices: 18703--18744 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18693 AACAGGTTTT
* *
18703 TAGCGGCGTTTTTTCGGAGCTA
1 TAGCGGCGTTTTTACGAAGCTA
18725 TAGCGGCGTTTTTAC-AAGCT
1 TAGCGGCGTTTTTACGAAGCT
18745 CCCAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.36
Consensus pattern (22 bp):
TAGCGGCGTTTTTACGAAGCTA
Found at i:18958 original size:78 final size:77
Alignment explanation
Indices: 18823--18966 Score: 180
Period size: 78 Copynumber: 1.9 Consensus size: 77
18813 AAACATGATC
* * * * *
18823 TTTAGTGACGTTTTTCCACAAACACCGCTAAAGAACATGATCTTTAACGGCGCTTTTCCAACAAA
1 TTTAGCGACGTTTTCCCACAAACACCGCTAAAAAACATGATCTTTAACGACACTTTTCCAACAAA
18888 CGCCGCTAAATT
66 CGCCGCTAAATT
* * ** * *
18900 TTTAGCGACGCTTTTCCCACAAACGCCGCTAAAAAACATGGTCTTTAGTGACATTTTTCCCACAA
1 TTTAGCGACG-TTTTCCCACAAACACCGCTAAAAAACATGATCTTTAACGACACTTTTCCAACAA
18965 AC
65 AC
18967 ACCACTAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
77 9 0.16
78 46 0.84
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (77 bp):
TTTAGCGACGTTTTCCCACAAACACCGCTAAAAAACATGATCTTTAACGACACTTTTCCAACAAA
CGCCGCTAAATT
Done.