Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005500.1 Hibiscus syriacus cultivar Beakdansim tig00012659_pilon, 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: 60276
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:18415 original size:2 final size:2
Alignment explanation
Indices: 18408--18462 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
18398 GATTTCTGTT
18408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18450 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
18463 ATGTGTTTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23385 original size:20 final size:20
Alignment explanation
Indices: 23360--23404 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
23350 TTATCCGGAA
**
23360 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAAGTTT
23380 AAAAATCCGGTCTGAAGTTT
1 AAAAATCCGGTCTGAAGTTT
23400 AAAAA
1 AAAAA
23405 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAAGTTT
Found at i:26550 original size:14 final size:14
Alignment explanation
Indices: 26531--26562 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
26521 TTTACGTTTT
26531 AAATTTAAGATTTA
1 AAATTTAAGATTTA
*
26545 AAATTTATGATTTA
1 AAATTTAAGATTTA
26559 AAAT
1 AAAT
26563 ATTTTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
AAATTTAAGATTTA
Found at i:27230 original size:3 final size:3
Alignment explanation
Indices: 27222--27266 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
27212 AAGGTTCGCC
27222 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27267 TGACATTCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28266 original size:2 final size:2
Alignment explanation
Indices: 28261--28310 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
28251 TATATTAATT
28261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28303 TA TA TA TA
1 TA TA TA TA
28311 AGATATTTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30261 original size:7 final size:7
Alignment explanation
Indices: 30251--30284 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
30241 TTGTAATATT
30251 TAATAAA
1 TAATAAA
30258 TAATAAA
1 TAATAAA
30265 TAAT-AA
1 TAATAAA
30271 TAAT-AA
1 TAATAAA
30277 TAATAAA
1 TAATAAA
30284 T
1 T
30285 TTAAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
TAATAAA
Found at i:30468 original size:45 final size:45
Alignment explanation
Indices: 30417--30505 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
30407 GGAAATGTTG
30417 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTA
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTA
30462 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTT
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTT
30506 GATAATATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTA
Found at i:30691 original size:46 final size:46
Alignment explanation
Indices: 30523--32020 Score: 2415
Period size: 46 Copynumber: 32.0 Consensus size: 46
30513 TCTAAAAGCT
* * * *
30523 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30570 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30615 CCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
**
30662 CTTGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
30708 CCCGAAGATTTTTGATAACATTATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* **
30754 CCTGAAGGTTTTTTTGAAAACATCATGCACTGAAACACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30802 CCCAAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30848 CCCGAAGGTTTTTAAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
30894 CCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
30942 CCTGAAGGTTTTTTTGAAAACATCATGCACTGAAAGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
30990 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31036 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31082 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31128 CCTGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31176 CCTGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG---TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31225 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31271 CCCGAAGG-TTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31316 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31362 CCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG---TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31411 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31457 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31503 CCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31551 CCTGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31599 CCCGAAGGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31645 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31691 CCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31739 CCTGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31787 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31833 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31879 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31925 CCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG---TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31974 CCCGAAGGTTTTTTTGAAAACATTATGCACTGAAGGACTTACAGATG
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
32021 TGGGAAATAG
Statistics
Matches: 1374, Mismatches: 57, Indels: 39
0.93 0.04 0.03
Matches are distributed among these distances:
45 85 0.06
46 705 0.51
47 51 0.04
48 394 0.29
49 139 0.10
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (46 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:31000 original size:188 final size:187
Alignment explanation
Indices: 30523--32020 Score: 2503
Period size: 188 Copynumber: 8.0 Consensus size: 187
30513 TCTAAAAGCT
* * * *
30523 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGG---TTTTGAA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAA
*
30585 AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTGAAAACATCATGCACTGAAGG
65 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTGAAAACATCATGCACTGAAGG
* **
30650 GCTTACAGATGACTTGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
130 ACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * * *
30708 CCCGAAGATTTTTGATAACATTATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
** *
30773 ACATCATGCACTGAAACACTTACAGATGACCCAAAGG-TTTTTGAAAACATCATGCACTGAAGGA
66 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGA
*
30837 CTTACAGATGACCCGAAGGTTTTTAAAAACATCATGCACTGAAGGACTTACAGATGA
131 CTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30894 CCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGA
1 CCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGA
*
30959 AAACATCATGCACTGAAAGACTTACAGATGACCCGAAGG-TTTTTGAAAACATCATGCACTGAAG
64 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTGAAAACATCATGCACTGAAG
* *
31023 GACTTACAGATGACCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
129 GACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31082 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
*
31147 ACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTTGAAAACATCATGCACTGAAG
66 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTTGAAAACATCATGCACTGAAG
31212 GACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
129 GACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31271 CCCGAAGG-TTTTGAAATCGTCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTGAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
31333 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAG
66 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTTGAAAACATCATGCACTGAAG
31398 GACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
129 GACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31457 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
*
31522 ACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGAAAACATCATGCACTGAAGG
66 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTTTGAAAACATCATGCACTGAAGG
*
31587 ACTTACAGATGACCCGAAGGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
130 ACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31645 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
*
31710 ACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGAAAACATCATGCACTGAAGG
66 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTTTGAAAACATCATGCACTGAAGG
31775 ACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
130 ACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31833 CCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTGAAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
31896 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAG
66 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTTGAAAACATCATGCACTGAAG
*
31961 GACTTACAGATGACCCGAAGGTTTTTTTGAAAACATTATGCACTGAAGGACTTACAGATG
129 GACTTACAGATGACCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
32021 TGGGAAATAG
Statistics
Matches: 1262, Mismatches: 37, Indels: 24
0.95 0.03 0.02
Matches are distributed among these distances:
184 39 0.03
185 7 0.01
186 364 0.29
187 134 0.11
188 547 0.43
189 171 0.14
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (187 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAAA
ACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGA
CTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:31017 original size:234 final size:231
Alignment explanation
Indices: 30523--32020 Score: 2421
Period size: 234 Copynumber: 6.4 Consensus size: 231
30513 TCTAAAAGCT
* * * * *
30523 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGG-TTTTGAAAA
1 CCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAA
* *
30587 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGGC
66 CATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGAC
** *
30652 TTACAGATGACTTGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGAT
130 TTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
30717 TTTTGATAACATTATGCACTGAAGGACTTACAGATGA
195 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* ** *
30754 CCTGAAGGTTTTTTTGAAAACATCATGCACTGAAACACTTACAGATGACCCAAAGGTTTTTGAAA
1 CCCGAAGG-TTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAA
*
30819 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTAAAAACATCATGCACTGAAGGAC
65 ACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGAC
*
30884 TTACAGATGACCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAG
130 TTACAGATGACCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
30949 GTTTTTTTGAAAACATCATGCACTGAAAGACTTACAGATGA
193 G--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
30990 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAT
1 CCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAA
*
31054 CGTCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACT
66 CATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACT
* *
31119 TACAGATGACCTGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGG
131 TACAGATGACCCGAAGG--TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
31184 TTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
194 ---TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31225 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAT
1 CCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAA
*
31288 CGTCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACT
66 CATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACT
31353 TACAGATGACCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 TACAGATGACCCGAAGG---TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
31418 GTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
193 GTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
31457 CCCGAAGG-TTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTGAA
1 CCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTGAA
*
31521 AACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGAAAACATCATGCACTGAAG
64 AACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTGAAAACATCATGCACTGAAG
*
31586 GACTTACAGATGACCCGAAGGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
127 GACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
* *
31651 GGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGA
192 GGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
31691 CCCGAAGGTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCTGAAGGTTTTTTTGA
1 CCCGAAGG-TTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTGA
31756 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGG
63 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGG
* *
31821 ACTTACAGATGACCCGAAGGTTTTTGAAATCGTCATGCACTGAAGGACTTACAGATGACCCGAAG
128 ACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
31886 GTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
193 GTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
31925 CCCGAAGGTTTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTTTG
1 CCCGAAGG--TTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTTG
*
31990 AAAACATTATGCACTGAAGGACTTACAGATG
62 AAAACATCATGCACTGAAGGACTTACAGATG
32021 TGGGAAATAG
Statistics
Matches: 1202, Mismatches: 49, Indels: 28
0.94 0.04 0.02
Matches are distributed among these distances:
231 7 0.01
232 171 0.14
233 44 0.04
234 535 0.45
235 267 0.22
236 132 0.11
237 46 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (231 bp):
CCCGAAGGTTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAA
CATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACT
TACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
TTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:32720 original size:22 final size:21
Alignment explanation
Indices: 32695--32773 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 21
32685 AATAAAGCTT
32695 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTT-AAAAAAGAATCTA
* *
32717 TCATCTTT-AAAGAGATAGGCTA
1 TCATCTTTAAAAAAGA-A-TCTA
* *
32739 TCATCTTTGAAGAAAGAGTCTA
1 TCATCTTT-AAAAAAGAATCTA
32761 TCATCTTTAAAAA
1 TCATCTTTAAAAA
32774 GTATAGATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 6 0.13
21 5 0.11
22 30 0.65
24 5 0.11
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (21 bp):
TCATCTTTAAAAAAGAATCTA
Found at i:34269 original size:75 final size:74
Alignment explanation
Indices: 34118--34257 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 74
34108 GATATAGGCC
* * * *
34118 TTCAACATGCCCCAACATTGGCTAATACAAGCATTCAAAATGCGTCAACATTCTTCATTCTGATT
1 TTCAACATGCCCCAACATTTGCTAATACAAG-ATTCAAAATACATCAACATTCATCATTCTGATT
34183 GAAAGGGGCT
65 GAAAGGGGCT
* * * *
34193 TTCAACATGCCCCAACATTTGCTGATA-TAGATGTTCAAAATACATCAACTTTCATGATTCTGAT
1 TTCAACATGCCCCAACATTTGCTAATACAAGA--TTCAAAATACATCAACATTCATCATTCTGAT
34257 T
64 T
34258 AAGATGGGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 1 0.02
74 2 0.04
75 52 0.95
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (74 bp):
TTCAACATGCCCCAACATTTGCTAATACAAGATTCAAAATACATCAACATTCATCATTCTGATTG
AAAGGGGCT
Found at i:43949 original size:17 final size:17
Alignment explanation
Indices: 43917--43949 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43907 CTACGGGCCA
43917 TTCTCTCATTTCCTCTT
1 TTCTCTCATTTCCTCTT
43934 TTCT-TCATTTCTCTCT
1 TTCTCTCATTTC-CTCT
43950 AAAAACGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (17 bp):
TTCTCTCATTTCCTCTT
Found at i:44792 original size:3 final size:3
Alignment explanation
Indices: 44775--44831 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
44765 TTGTAATATT
*
44775 TAA TAAA TAA T-A TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44820 TAA TAA TAA TAA
1 TAA TAA TAA TAA
44832 ATTTAAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:47377 original size:15 final size:14
Alignment explanation
Indices: 47352--47387 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
47342 AATTTAATCA
*
47352 TAAAAATATATTTT
1 TAAATATATATTTT
47366 TAATATATATATTTT
1 TAA-ATATATATTTT
47381 TAAATAT
1 TAAATAT
47388 GAATTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAATATATATTTT
Found at i:47386 original size:16 final size:15
Alignment explanation
Indices: 47357--47387 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47347 AATCATAAAA
47357 ATATATTTTTAATAT
1 ATATATTTTTAATAT
47372 ATATATTTTTAA-AT
1 ATATATTTTTAATAT
47386 AT
1 AT
47388 GAATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATATTTTTAATAT
Found at i:47477 original size:2 final size:2
Alignment explanation
Indices: 47470--47496 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47460 TATAAGGATC
47470 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
47497 CACACACACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48162 original size:2 final size:2
Alignment explanation
Indices: 48155--48184 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
48145 AACTCTCAAC
48155 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48185 CACATCGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51787 original size:18 final size:19
Alignment explanation
Indices: 51766--51812 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
51756 GCAAATTTTG
*
51766 GTATCGATACTCAA-GTGA
1 GTATCGATACCCAAGGTGA
51784 GTATCGATACCCAAGGGGTGA
1 GTATCGATACCCAA--GGTGA
51805 GTATCGAT
1 GTATCGAT
51813 GTTGTTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 13 0.52
21 12 0.48
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (19 bp):
GTATCGATACCCAAGGTGA
Found at i:52645 original size:46 final size:46
Alignment explanation
Indices: 52578--52669 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
52568 ATTTGCAGAG
52578 TATGTCTTGAGTATTTGTAGAGGTATGGTTGTGATGTACGTATTTT
1 TATGTCTTGAGTATTTGTAGAGGTATGGTTGTGATGTACGTATTTT
52624 TATGTCTTGAGTATTTGTAGAGGTATGGTTGTGATGTACGTATTTT
1 TATGTCTTGAGTATTTGTAGAGGTATGGTTGTGATGTACGTATTTT
52670 GGAGGACTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.20, C:0.04, G:0.28, T:0.48
Consensus pattern (46 bp):
TATGTCTTGAGTATTTGTAGAGGTATGGTTGTGATGTACGTATTTT
Found at i:54438 original size:10 final size:10
Alignment explanation
Indices: 54423--54457 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
54413 CAGTAGCTTT
54423 TCCCATGTCG
1 TCCCATGTCG
54433 TCCCATG-CG
1 TCCCATGTCG
54442 -CCCATGTCG
1 TCCCATGTCG
54451 TCCCATG
1 TCCCATG
54458 CGTGTGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.26
9 4 0.17
10 13 0.57
ACGTcount: A:0.11, C:0.43, G:0.20, T:0.26
Consensus pattern (10 bp):
TCCCATGTCG
Found at i:54447 original size:18 final size:18
Alignment explanation
Indices: 54424--54459 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54414 AGTAGCTTTT
54424 CCCATGTCGTCCCATGCG
1 CCCATGTCGTCCCATGCG
54442 CCCATGTCGTCCCATGCG
1 CCCATGTCGTCCCATGCG
54460 TGTGAATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.44, G:0.22, T:0.22
Consensus pattern (18 bp):
CCCATGTCGTCCCATGCG
Done.